AlloSure SNP Error Analysis



J. Collins | 2017-04-11

In [1]:
from collections import defaultdict, OrderedDict
from datetime import datetime
from math import log, sqrt
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.font_manager import FontProperties
from matplotlib.gridspec import GridSpec
from matplotlib.ticker import FuncFormatter
from operator import itemgetter
from scipy.stats import binom, norm, poisson
from tqdm import tqdm
import ggplot
import matplotlib as mpl
import matplotlib.mlab as mlabS
import matplotlib.pyplot as plt
import numpy as np
import os
import pandas as pd
import plotly
import random
import re
import seaborn as sns
import sys
import timeit

sns.set_style('whitegrid')
sns.set(font_scale=1.4)

%matplotlib inline
In [3]:
# from notebook.services.config import ConfigManager
# ConfigManager().update('notebook', {'ExecuteTime': {
#        'display_absolute_timestamps': False,
#        'display_absolute_timings': False,
#     'relative_timing_update_period': .005,
#     'template': {
#         'executed': 'started ${start_time}, finished in ${end_time}-${duration}',
#     }
# }})
In [48]:
import plotly.plotly as py
import cufflinks as cf

cf.set_config_file(offline=True, world_readable=True, theme='ggplot')

function definitions

In [2]:
# * * * ADD CUSTOM FUNCTIONS TO CFDNA_TOOLS MODULE * * *


def print_exec_time(init_time):
    '''Function defintion to track total time taken for 
       a given cell to complete its execution.
    '''
    elapsed = timeit.default_timer() - init_time
    print("Execution time: {} ms ".format(round(elapsed * 1000, 5)))


def mpl_reset():
    '''Undo Seaborn style'''
    del sns
    mpl.rcParams.update(mpl.rcParamsDefault)


def to_percent(y, position):
    '''Print dd-cfDNA labels in percentage.'''
    # Ignore the passed in position. This has the effect of scaling the default
    # tick locations.
    s = str(100 * y)
    # The percent symbol needs escaping in latex
    if mpl.rcParams['text.usetex'] is True:
        return s + r'$\%$'
    else:
        return s + '%'


def strip_all_whitespace(df):
    for col in df.columns:
        if df[col].dtype == object:
            tmp_s = df[col].str.strip()
            df.loc[:, col] = tmp_s
    return df


def convert_result_to_float(df, col_name, div=1):
    def f(x): return float(x) / div
    for col in df.columns:
        if col.endswith(col_name):
            tmp_s = df[col].str.replace('%', '')
            df.loc[:, col] = tmp_s.apply(f)
    return df


def return_numeric(df):
    return df_all.select_dtypes(
        include=['float64']).dropna(
        how='all',
        axis=1)


def t_init():
    return timeit.default_timer()
In [3]:
def distribute(series, n=100, set_xlim=True, p=97):
    sns.set_style('white')
    s = series.dropna()
    fig, ax1 = plt.subplots(nrows=1,
                            ncols=1,
                            figsize=(8, 8))
    y, x, _ = ax1.hist(
        s,
        bins=n,
        normed=True,
        fc='w',
        ec='k',
        lw=1.0,
        zorder=3,
        alpha=0.7,
        label='{}'.format(
            s.describe(
                percentiles=[0.05, 0.1, 0.25,
                             0.5, 0.75, 0.9,
                             0.95])))
    ax2 = ax1.twinx()
    mean = s.clip_upper(0.01).median()
    s_linx = np.linspace(min(s),
                         np.percentile(s, 95),
                         100)
    ax1.plot(s_linx,
             norm.pdf(s_linx,
                      loc=mean,
                      scale=s.clip_upper(0.01).std()),
             '--k', lw=2.0, zorder=5)
    ax2.plot(s_linx,
             poisson.pmf(np.arange(100),
                         mu=mean * (1e2 / max(s_linx))),
             '--', c='maroon', lw=2.0, zorder=6,
             label="poisson")
    for ax in (ax1, ax2):
        ax.xaxis.set_ticks_position('bottom')
        ax.set_xlim(min(s), max(s_linx))
        ax.spines['top'].set_visible(False)
        ax.xaxis.set_ticks_position('bottom')
        ax.tick_params('both',
                       width=1,
                       which='major',)
    ax.tick_params('y',
                   length=15,
                   colors='maroon',
                   pad=40,)
    ax1.legend(loc='best',
               bbox_to_anchor=(1, 1))
    sns.despine(ax=ax1,
                offset=10,
                trim=True)
    sns.despine(ax=ax2,
                offset=10,
                trim=True)
    fig.tight_layout()

['size', 'width', 'color', 'tickdir', 'pad', 'labelsize', 'labelcolor', 'zorder', 'gridOn', 'tick1On', 'tick2On', 'label1On', 'label2On', 'length', 'direction', 'left', 'bottom', 'right', 'top', 'labelleft', 'labelbottom', 'labelright', 'labeltop']

pandas display options

In [4]:
pd.set_option('display.max_columns', 200)
pd.set_option('display.max_colwidth', 500)
pd.set_option('display.max_rows', 240)
pd.set_option('display.width', 100)
In [34]:
# autopep8 -dv -a -a
# pip install jupyter_contrib_nbextensions
# jupyter nbextensions_configurator enable
In [93]:
AV_all_smpls_list = pd.read_clipboard().Sample.values
AV_all_smpls_list
Out[93]:
array(['153B1A-Oct-26-15', '153B1B-Oct-26-15', '153B1C-Oct-27-15', ...,
       'WC44-14-07a-2-41092', 'TE93-34-45b-2-42353', 'NO56-89-30b-2-42354'], dtype=object)

i/o file paths

In [5]:
# File input pathnames:
# seq01_smpl     = '/Users/jcollins-macbook/Python/cfDNA/stanford/gallo-klvtx/CFDNA_SAMPLE_RESULT_REFLAB_MVW_01102017a.txt'
# seq01_SNP      = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/CFDNA_SNP_RESULT_T1.txt'
# seq01_smpl     = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/CFDNA_SAMPLE_RESULT_REFLAB_MVW_170201.csv'
# seq01_SNP      = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/CFDNA_SNP_RESULT_T1_170201.csv'

seq01_smpl       = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/caredx/Datasets/tertiary/170215_all_outputBySample.csv'
KT_smpl          = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/caredx/AlloSure--Analytical_Validation/PCR-Multiplexing-project/KT170203_SDU_output_updated 170308.txt'

seq01_SNP        = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/caredx/Datasets/tertiary/170215_all_outputBySNP.csv'
# seq01_SNP      = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/caman trredx/Datasets/tertiary/CFDNA_SNP_RESULT_T1-2017_output.txt'
DART_lock2_smpls = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/caredx/Datasets/dart/DART_28Oct2017lock_eids.csv'
DART_lock2_PIDs  = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/caredx/Datasets/dart/DART_28Oct2017lock_eids_sid.csv'
SNP_MiSeq_cov    = '/Users/jcollins-macbook/Documents/iCloud-cfDNA/caredx/AlloSure--Analytical_Validation/PCR-Multiplexing-project/coverage-uniformity/282_amplicons_2X-vs-1X-coverage.csv'
In [6]:
SNP_cov = pd.read_csv(SNP_MiSeq_cov)
SNP_cov.set_index('SNP_ID', inplace=True)
SNP_cov
Out[6]:
Genome_location Ref_start_pos Ref_end_pos rsID SNP_pos_in_ref Ref Alt amp_length SNP_pos SNP_cov_end_bound SNP_cov_type
SNP_ID
IISNP1 chr11_115206646_115207761 501 616 rs10488710 chr11_115206646_115207761:531 C G 116 31 35 False
IISNP10 chr4_46329095_46330254 501 660 rs279844 chr4_46329095_46330254:561 A T 160 61 79 False
IISNP100 chr19_10599851_10600965 501 615 rs1048290 chr19_10599851_10600965:592 G C 115 92 34 False
IISNP101 chr17_33998221_33999330 501 610 rs1049379 chr17_33998221_33999330:582 G C 110 82 29 True
IISNP102 chr1_154744236_154745348 501 613 rs1051614 chr1_154744236_154745348:572 C G 113 72 32 True
IISNP103 chr2_118574685_118575803 501 619 rs1052637 chr2_118574685_118575803:531 C G 119 31 38 False
IISNP104 chr1_236381266_236382387 501 622 rs1055851 chr1_236381266_236382387:560 G C 122 60 41 True
IISNP105 chr20_24939035_24940159 501 625 rs1056033 chr20_24939035_24940159:556 G C 125 56 44 True
IISNP106 chr5_145441622_145442735 501 614 rs1056149 chr5_145441622_145442735:582 G C 114 82 33 True
IISNP107 chr11_17519170_17520279 501 610 rs1064074 chr11_17519170_17520279:573 C G 110 73 29 True
IISNP108 chr2_85769181_85770292 501 612 rs1078004 chr2_85769181_85770292:531 C G 112 31 31 False
IISNP109 chr11_11292148_11293259 501 612 rs10831567 chr11_11292148_11293259:553 G C 112 53 31 True
IISNP11 chr4_169663057_169664186 501 630 rs6811238 chr4_169663057_169664186:559 T G 130 59 49 True
IISNP110 chr10_129899187_129900315 501 629 rs11106 chr10_129899187_129900315:592 G C 129 92 48 False
IISNP111 chr1_75096893_75098000 501 608 rs11210490 chr1_75096893_75098000:534 G C 108 34 27 True
IISNP112 chr7_130020932_130022055 501 624 rs1126899 chr7_130020932_130022055:557 G C 124 57 43 True
IISNP113 chr15_78632267_78633388 501 622 rs1127472 chr15_78632267_78633388:564 C G 122 64 41 True
IISNP114 chr10_24872787_24873906 501 620 rs1127893 chr10_24872787_24873906:583 C G 120 83 39 False
IISNP115 chr5_176862952_176864062 501 611 rs1130857 chr5_176862952_176864062:568 G C 111 68 30 True
IISNP116 chr4_88415067_88416171 501 605 rs1049544 chr4_88415067_88416171:570 G C 105 70 24 True
IISNP117 chr19_44302506_44303626 501 621 rs11547806 chr19_44302506_44303626:561 C G 121 61 40 True
IISNP118 chr12_121416065_121417194 501 630 rs1169289 chr12_121416065_121417194:558 C G 130 58 49 True
IISNP119 chr9_2717972_2719101 501 630 rs12237048 chr9_2717972_2719101:563 C G 130 63 49 True
IISNP12 chr16_78016473_78017602 501 630 rs430046 chr16_78016473_78017602:579 C T 130 79 49 True
IISNP120 chr4_129042633_129043755 501 623 rs12508837 chr4_129042633_129043755:572 C G 123 72 42 True
IISNP121 chr10_5136059_5137186 501 628 rs12529 chr10_5136059_5137186:593 C G 128 93 47 False
IISNP122 chr6_170861722_170862832 501 611 rs12717 chr6_170861722_170862832:579 G C 111 79 30 True
IISNP123 chr5_161118544_161119671 501 628 rs13184586 chr5_161118544_161119671:582 C G 128 82 47 True
IISNP124 chr9_129455060_129456167 501 608 rs13295990 chr9_129455060_129456167:528 G C 108 28 27 True
IISNP125 chr13_25008849_25009978 501 630 rs13428 chr13_25008849_25009978:593 C G 130 93 49 False
IISNP126 chr19_48620482_48621601 501 620 rs13436 chr19_48620482_48621601:555 C G 120 55 39 True
IISNP127 chr11_57798787_57799916 501 630 rs1374570 chr11_57798787_57799916:585 G C 130 85 49 False
IISNP128 chr3_16305112_16306238 501 627 rs14080 chr3_16305112_16306238:563 C G 127 63 46 True
IISNP129 chr9_125315189_125316306 501 618 rs1411271 chr9_125315189_125316306:590 G C 118 90 37 False
IISNP13 chr19_39559236_39560337 501 602 rs576261 chr19_39559236_39560337:572 A C 102 72 21 True
IISNP130 chr19_618466_619585 501 620 rs14155 chr19_618466_619585:556 G C 120 56 39 True
IISNP131 chr1_247751483_247752601 501 619 rs1151687 chr1_247751483_247752601:537 G C 119 37 38 False
IISNP132 chr12_49255241_49256366 501 626 rs1565933 chr12_49255241_49256366:558 G C 126 58 45 True
IISNP133 chr12_14656198_14657327 501 630 rs1600 chr12_14656198_14657327:571 G C 130 71 49 True
IISNP134 chr6_38781300_38782411 501 612 rs1678690 chr6_38781300_38782411:567 C G 112 67 31 True
IISNP135 chr2_29415814_29416943 501 630 rs1881421 chr2_29415814_29416943:553 G C 130 53 49 True
IISNP136 chr19_44981323_44982437 501 615 rs1897820 chr19_44981323_44982437:561 C G 115 61 34 True
IISNP137 chr15_40655304_40656417 501 614 rs1898882 chr15_40655304_40656417:570 G C 114 70 33 True
IISNP138 chr21_40669882_40670990 501 609 rs2056844 chr21_40669882_40670990:579 G C 109 79 28 True
IISNP139 chr8_23058791_23059898 501 608 rs20575 chr8_23058791_23059898:534 C G 108 34 27 True
IISNP14 chr8_28410486_28411610 501 625 rs10092491 chr8_28410486_28411610:587 T C 125 87 44 False
IISNP140 chr21_47849924_47851051 501 628 rs2070426 chr21_47849924_47851051:561 G C 128 61 47 True
IISNP141 chr6_33272320_33273427 501 608 rs2071888 chr6_33272320_33273427:536 G C 108 36 27 True
IISNP142 chr12_31249317_31250444 501 628 rs2075322 chr12_31249317_31250444:545 C G 128 45 47 False
IISNP143 chr6_52617161_52618275 501 615 rs2180314 chr6_52617161_52618275:571 C G 115 71 34 True
IISNP144 chr6_41773010_41774136 501 627 rs2185798 chr6_41773010_41774136:567 G C 127 67 46 True
IISNP145 chr12_5020815_5021938 501 624 rs2227910 chr12_5020815_5021938:534 G C 124 34 43 False
IISNP146 chr9_137711436_137712561 501 626 rs2228560 chr9_137711436_137712561:562 G C 126 62 45 True
IISNP147 chr2_215644872_215645995 501 624 rs2229571 chr2_215644872_215645995:593 C G 124 93 43 False
IISNP148 chr2_75113219_75114341 501 623 rs2229627 chr2_75113219_75114341:571 C G 123 71 42 True
IISNP149 chr3_129285829_129286957 501 629 rs2245285 chr3_129285829_129286957:585 G C 129 85 48 False
IISNP15 chr16_5868144_5869263 501 620 rs2342747 chr16_5868144_5869263:557 A G 120 57 39 True
IISNP150 chr21_44293171_44294278 501 608 rs2248490 chr21_44293171_44294278:574 C G 108 74 27 True
IISNP151 chr7_150877678_150878790 501 613 rs2253592 chr7_150877678_150878790:583 C G 113 83 32 False
IISNP152 chr1_22216012_22217133 501 622 rs2254357 chr1_22216012_22217133:593 C G 122 93 41 False
IISNP153 chr14_58563143_58564270 501 628 rs2273442 chr14_58563143_58564270:552 G C 128 52 47 True
IISNP154 chr10_99438974_99440086 501 613 rs2275047 chr10_99438974_99440086:568 G C 113 68 32 True
IISNP155 chr12_130940594_130941723 501 630 rs2277361 chr12_130940594_130941723:557 G C 130 57 49 True
IISNP156 chr12_56827164_56828284 501 621 rs2279665 chr12_56827164_56828284:531 C G 121 31 40 False
IISNP157 chr9_8388794_8389902 501 609 rs2279776 chr9_8388794_8389902:571 C G 109 71 28 True
IISNP158 chr22_37963741_37964868 501 628 rs2281098 chr22_37963741_37964868:559 C G 128 59 47 True
IISNP159 chr19_10083723_10084832 501 610 rs2287813 chr19_10083723_10084832:570 C G 110 70 29 True
IISNP16 chr3_32417091_32418199 501 609 rs4364205 chr3_32417091_32418199:554 T G 109 54 28 True
IISNP160 chr17_76448943_76450062 501 620 rs2289751 chr17_76448943_76450062:563 G C 120 63 39 True
IISNP161 chr15_22960301_22961425 501 625 rs2289818 chr15_22960301_22961425:568 G C 125 68 44 True
IISNP162 chr1_87100813_87101939 501 627 rs2292830 chr1_87100813_87101939:563 C G 127 63 46 True
IISNP163 chr8_27667377_27668505 501 629 rs2294092 chr8_27667377_27668505:593 C G 129 93 48 False
IISNP164 chr6_126277677_126278784 501 608 rs2295005 chr6_126277677_126278784:554 G C 108 54 27 True
IISNP165 chr10_90342263_90343376 501 614 rs2296545 chr10_90342263_90343376:575 C G 114 75 33 True
IISNP166 chr7_138739465_138740586 501 622 rs2297236 chr7_138739465_138740586:573 G C 122 73 41 True
IISNP167 chr7_156761669_156762794 501 626 rs2302443 chr7_156761669_156762794:556 G C 126 56 45 True
IISNP168 chr16_88767192_88768321 501 630 rs2306049 chr16_88767192_88768321:578 G C 130 78 49 True
IISNP169 chr22_45821381_45822501 501 621 rs1022478 chr22_45821381_45822501:576 C G 121 76 40 True
IISNP17 chr20_15124404_15125523 501 620 rs445251 chr20_15124404_15125523:530 G C 120 30 39 False
IISNP170 chr17_15216858_15217965 501 608 rs230898 chr17_15216858_15217965:580 C G 108 80 27 True
IISNP171 chr19_36277889_36279010 501 622 rs231235 chr19_36277889_36279010:582 C G 122 82 41 True
IISNP172 chr6_150209159_150210278 501 620 rs2342767 chr6_150209159_150210278:559 C G 120 59 39 True
IISNP173 chr20_5903313_5904421 501 609 rs236152 chr20_5903313_5904421:536 C G 109 36 28 True
IISNP174 chr3_48460757_48461883 501 627 rs2362450 chr3_48460757_48461883:557 C G 127 57 46 True
IISNP175 chr2_27324182_27325292 501 611 rs2384571 chr2_27324182_27325292:543 G C 111 43 30 True
IISNP176 chr5_75932415_75933522 501 608 rs2455230 chr5_75932415_75933522:551 G C 108 51 27 True
IISNP177 chr5_140531170_140532269 501 600 rs246703 chr5_140531170_140532269:577 C G 100 77 19 True
IISNP178 chr10_25700758_25701869 501 612 rs2480345 chr10_25700758_25701869:584 C G 112 84 31 False
IISNP179 chr5_78339702_78340831 501 630 rs248385 chr5_78339702_78340831:556 C G 130 56 49 True
IISNP18 chr9_27985366_27986466 501 601 rs7041158 chr9_27985366_27986466:573 C T 101 73 20 True
IISNP180 chr1_62516111_62517226 501 616 rs2498982 chr1_62516111_62517226:573 G C 116 73 35 True
IISNP181 chr10_38344113_38345242 501 630 rs2505232 chr10_38344113_38345242:588 C G 130 88 49 False
IISNP182 chr11_94230690_94231811 501 622 rs2509943 chr11_94230690_94231811:568 C G 122 68 41 True
IISNP183 chr16_4309882_4311001 501 620 rs251732 chr16_4309882_4311001:587 C G 120 87 39 False
IISNP184 chr9_136536239_136537346 501 608 rs2519123 chr9_136536239_136537346:555 C G 108 55 27 True
IISNP185 chr7_25194102_25195226 501 625 rs2523072 chr7_25194102_25195226:564 G C 125 64 44 True
IISNP186 chr18_44560549_44561667 501 619 rs2571028 chr18_44560549_44561667:552 C G 119 52 38 True
IISNP187 chr11_4566780_4567909 501 630 rs2657167 chr11_4566780_4567909:556 C G 130 56 49 True
IISNP188 chr8_143694218_143695347 501 630 rs28686812 chr8_143694218_143695347:558 G C 130 58 49 True
IISNP189 chr10_126714134_126715248 501 615 rs2946994 chr10_126714134_126715248:581 G C 115 81 34 True
IISNP19 chr1_233447873_233448982 501 610 rs1294331 chr1_233447873_233448982:541 C T 110 41 29 True
IISNP190 chr19_53343564_53344688 501 625 rs10419826 chr19_53343564_53344688:555 C G 125 55 44 True
IISNP191 chr11_125763182_125764289 501 608 rs3088241 chr11_125763182_125764289:565 C G 108 65 27 True
IISNP192 chr17_35901690_35902813 501 624 rs3110623 chr17_35901690_35902813:536 C G 124 36 43 False
IISNP193 chr7_12268849_12269978 501 630 rs3173615 chr7_12268849_12269978:569 C G 130 69 49 True
IISNP194 chr16_11773071_11774198 501 628 rs3190321 chr16_11773071_11774198:592 C G 128 92 47 False
IISNP195 chr22_31490725_31491854 501 630 rs3205187 chr22_31490725_31491854:571 G C 130 71 49 True
IISNP196 chr4_77660183_77661297 501 615 rs344141 chr4_77660183_77661297:549 C G 115 49 34 True
IISNP197 chr4_186379303_186380429 501 627 rs35596415 chr4_186379303_186380429:597 G C 127 97 46 False
IISNP198 chr22_22868645_22869769 501 625 rs362124 chr22_22868645_22869769:565 C G 125 65 44 True
IISNP199 chr19_54663644_54664769 501 626 rs36657 chr19_54663644_54664769:566 G C 126 66 45 True
IISNP2 chr3_113804421_113805528 501 608 rs1872575 chr3_113804421_113805528:559 G A 108 59 27 True
IISNP20 chr5_17374335_17375441 501 607 rs159606 chr5_17374335_17375441:564 A G 107 64 26 True
IISNP200 chr2_219601952_219603075 501 624 rs3731877 chr2_219601952_219603075:548 G C 124 48 43 True
IISNP201 chr2_220378975_220380095 501 621 rs3731909 chr2_220378975_220380095:586 C G 121 86 40 False
IISNP202 chr6_76659989_76661118 501 630 rs3734311 chr6_76659989_76661118:563 G C 130 63 49 True
IISNP203 chr7_20180151_20181280 501 630 rs3735615 chr7_20180151_20181280:567 C G 130 67 49 True
IISNP204 chr10_128018457_128019577 501 621 rs3740199 chr10_128018457_128019577:569 C G 121 69 40 True
IISNP205 chr2_101009515_101010629 501 615 rs3748930 chr2_101009515_101010629:568 G C 115 68 34 True
IISNP206 chr11_8946706_8947820 501 615 rs3751066 chr11_8946706_8947820:578 G C 115 78 34 True
... ... ... ... ... ... ... ... ... ... ... ...
IISNP245 chr11_117163245_117164370 501 626 rs638405 chr11_117163245_117164370:580 C G 126 80 45 True
IISNP246 chr6_56482232_56483352 501 621 rs6459166 chr6_56482232_56483352:570 C G 121 70 40 True
IISNP247 chr6_138412785_138413907 501 623 rs648802 chr6_138412785_138413907:549 G C 123 49 42 True
IISNP248 chr19_57837471_57838600 501 630 rs6510057 chr19_57837471_57838600:548 C G 130 48 49 False
IISNP249 chr3_186917177_186918300 501 624 rs6764714 chr3_186917177_186918300:575 C G 124 75 43 True
IISNP25 chr11_5098168_5099267 501 600 rs10768550 chr11_5098168_5099267:547 C T 100 47 19 True
IISNP250 chr3_14755064_14756187 501 624 rs6790129 chr3_14755064_14756187:554 C G 124 54 43 True
IISNP251 chr3_45052203_45053327 501 625 rs6794 chr3_45052203_45053327:573 G C 125 73 44 True
IISNP252 chr3_183777454_183778574 501 621 rs6807362 chr3_183777454_183778574:557 G C 121 57 40 True
IISNP253 chr4_139139958_139141085 501 628 rs6838248 chr4_139139958_139141085:537 G C 128 37 47 False
IISNP254 chr7_141672808_141673933 501 626 rs713598 chr7_141672808_141673933:538 C G 126 38 45 False
IISNP255 chr14_50798535_50799661 501 627 rs7161563 chr14_50798535_50799661:592 G C 127 92 46 False
IISNP256 chr10_114052989_114054096 501 608 rs726009 chr10_114052989_114054096:558 C G 108 58 27 True
IISNP257 chr1_214836531_214837646 501 616 rs7289 chr1_214836531_214837646:580 C G 116 80 35 True
IISNP258 chr12_14018199_14019328 501 630 rs7301328 chr12_14018199_14019328:579 G C 130 79 49 True
IISNP259 chr13_73348771_73349897 501 627 rs7332388 chr13_73348771_73349897:589 G C 127 89 46 False
IISNP26 chr12_130761129_130762238 501 610 rs10773760 chr12_130761129_130762238:568 A G 110 68 29 True
IISNP260 chr22_51063487_51064595 501 609 rs743616 chr22_51063487_51064595:553 G C 109 53 28 True
IISNP261 chr6_36286765_36287879 501 615 rs743852 chr6_36286765_36287879:548 G C 115 48 34 True
IISNP262 chr17_71232306_71233435 501 630 rs745142 chr17_71232306_71233435:576 G C 130 76 49 True
IISNP263 chr6_46107197_46108304 501 608 rs7451713 chr6_46107197_46108304:556 C G 108 56 27 True
IISNP264 chr1_205553518_205554618 501 601 rs7526132 chr1_205553518_205554618:568 G C 101 68 20 True
IISNP265 chr1_47799106_47800221 501 616 rs7543016 chr1_47799106_47800221:534 G C 116 34 35 False
IISNP266 chr2_28824241_28825363 501 623 rs7601771 chr2_28824241_28825363:553 C G 123 53 42 True
IISNP267 chr7_4026399_4027521 501 623 rs7785899 chr7_4026399_4027521:546 C G 123 46 42 True
IISNP268 chr1_111956532_111957661 501 630 rs7825 chr1_111956532_111957661:566 C G 130 66 49 True
IISNP269 chr14_103439920_103441032 501 613 rs8009219 chr14_103439920_103441032:554 G C 113 54 32 True
IISNP27 chr9_137416746_137417845 501 600 rs10776839 chr9_137416746_137417845:563 G T 100 63 19 True
IISNP270 chr15_94883526_94884639 501 614 rs8025851 chr15_94883526_94884639:583 G C 114 83 33 False
IISNP271 chr16_16278312_16279424 501 613 rs8058696 chr16_16278312_16279424:558 G C 113 58 32 True
IISNP272 chr17_48625341_48626470 501 630 rs8076632 chr17_48625341_48626470:588 C G 130 88 49 False
IISNP273 chr16_8952508_8953628 501 621 rs8097 chr16_8952508_8953628:574 C G 121 74 40 True
IISNP274 chr19_18377056_18378185 501 630 rs8103906 chr19_18377056_18378185:592 G C 130 92 49 False
IISNP275 chr1_17659939_17661046 501 608 rs874881 chr1_17659939_17661046:561 G C 108 61 27 True
IISNP276 chr12_88440104_88441233 501 630 rs9262 chr12_88440104_88441233:573 G C 130 73 49 True
IISNP277 chr3_118866464_118867580 501 617 rs9289122 chr3_118866464_118867580:584 C G 117 84 36 False
IISNP278 chr17_42475406_42476535 501 630 rs936019 chr17_42475406_42476535:578 G C 130 78 49 True
IISNP279 chr6_26508757_26509875 501 619 rs9393728 chr6_26508757_26509875:574 C G 119 74 38 True
IISNP28 chr2_10085153_10086253 501 601 rs1109037 chr2_10085153_10086253:570 G A 101 70 20 True
IISNP280 chr11_60700573_60701681 501 609 rs9513 chr11_60700573_60701681:564 C G 109 64 28 True
IISNP281 chr19_56422500_56423625 501 626 rs977070 chr19_56422500_56423625:575 C G 126 75 45 True
IISNP282 chr3_112642035_112643149 501 615 rs9865242 chr3_112642035_112643149:534 C G 115 34 34 False
IISNP29 chr20_16240863_16241962 501 600 rs12480506 chr20_16240863_16241962:554 A G 100 54 19 True
IISNP3 chr1_160786113_160787219 501 607 rs560681 chr1_160786113_160787219:558 A G 107 58 26 True
IISNP30 chr2_182412681_182413789 501 609 rs12997453 chr2_182412681_182413789:579 A G 109 79 28 True
IISNP31 chr4_76425332_76426441 501 610 rs13134862 chr4_76425332_76426441:565 G A 110 65 29 True
IISNP32 chr6_12059397_12060504 501 608 rs13218440 chr6_12059397_12060504:558 G A 108 58 27 True
IISNP33 chr6_94536699_94537824 501 626 rs1336071 chr6_94536699_94537824:557 T C 126 57 45 True
IISNP34 chr6_123894407_123895512 501 606 rs1358856 chr6_123894407_123895512:572 C A 106 72 25 True
IISNP35 chr10_97172060_97173166 501 607 rs1410059 chr10_97172060_97173166:536 T C 107 36 26 True
IISNP36 chr6_120560128_120561231 501 604 rs1478829 chr6_120560128_120561231:567 T A 104 67 23 True
IISNP37 chr1_4366758_4367875 501 618 rs1490413 chr1_4366758_4367875:566 G A 118 66 37 True
IISNP38 chr11_5708471_5709577 501 607 rs1498553 chr11_5708471_5709577:558 C T 107 58 26 True
IISNP39 chr20_51295583_51296712 501 630 rs1523537 chr20_51295583_51296712:580 T C 130 80 49 True
IISNP4 chr8_144656177_144657285 501 609 rs4606077 chr8_144656177_144657285:578 T C 109 78 28 True
IISNP40 chr4_157489335_157490443 501 609 rs1554472 chr4_157489335_157490443:572 G A 109 72 28 True
IISNP41 chr18_55225209_55226308 501 600 rs1736442 chr18_55225209_55226308:569 T C 100 69 19 True
IISNP42 chr15_39312848_39313954 501 607 rs1821380 chr15_39312848_39313954:555 C G 107 55 26 True
IISNP43 chr4_10968504_10969612 501 609 rs2046361 chr4_10968504_10969612:556 T A 109 56 28 True
IISNP44 chr22_23801605_23802709 501 605 rs2073383 chr22_23801605_23802709:567 T C 105 67 24 True
IISNP45 chr6_152697130_152698240 501 611 rs214955 chr6_152697130_152698240:577 C T 111 77 30 True
IISNP46 chr17_41286243_41287360 501 618 rs2175957 chr17_41286243_41287360:580 T G 118 80 37 True
IISNP47 chr12_6908891_6910000 501 610 rs2255301 chr12_6908891_6910000:552 T C 110 52 29 True
IISNP48 chr12_6945352_6946456 501 605 rs2269355 chr12_6945352_6946456:563 C G 105 63 24 True
IISNP49 chr9_14746585_14747714 501 630 rs2270529 chr9_14746585_14747714:549 T C 130 49 49 False
IISNP5 chr12_40862467_40863585 501 619 rs2920816 chr12_40862467_40863585:586 A G 119 86 38 False
IISNP50 chr6_148760890_148761999 501 610 rs2272998 chr6_148760890_148761999:567 G C 110 67 29 True
IISNP51 chr17_80525564_80526669 501 606 rs2291395 chr17_80525564_80526669:576 A G 106 76 25 True
IISNP52 chr17_80765219_80766321 501 603 rs2292972 chr17_80765219_80766321:570 T C 103 70 22 True
IISNP53 chr3_110300565_110301664 501 600 rs2399332 chr3_110300565_110301664:562 T G 100 62 19 True
IISNP54 chr6_127462805_127463913 501 609 rs2503107 chr6_127462805_127463913:572 C A 109 72 28 True
IISNP55 chr20_23016527_23017635 501 609 rs2567608 chr20_23016527_23017635:556 T C 109 56 28 True
IISNP56 chr6_55155134_55156239 501 606 rs2811231 chr6_55155134_55156239:571 C A 106 71 25 True
IISNP57 chr21_33582165_33583274 501 610 rs2833736 chr21_33582165_33583274:558 G A 110 58 29 True
IISNP58 chr5_169735367_169736476 501 610 rs315791 chr5_169735367_169736476:554 A C 110 54 29 True
IISNP59 chr7_137029274_137030380 501 607 rs321198 chr7_137029274_137030380:565 T C 107 65 26 True
IISNP6 chr7_4309792_4310920 501 629 rs6955448 chr7_4309792_4310920:574 C T 129 74 48 True
IISNP60 chr5_178690152_178691259 501 608 rs338882 chr5_178690152_178691259:574 G A 108 74 27 True
IISNP61 chr17_80739299_80740406 501 608 rs3744163 chr17_80739299_80740406:561 G C 108 61 27 True
IISNP62 chr10_17192789_17193898 501 610 rs3780962 chr10_17192789_17193898:558 A G 110 58 29 True
IISNP63 chr8_136838646_136839775 501 630 rs4288409 chr8_136838646_136839775:584 A C 130 84 49 False
IISNP64 chr14_104768569_104769678 501 610 rs4530059 chr14_104768569_104769678:581 G A 110 81 29 True
IISNP65 chr21_28022802_28023902 501 601 rs464663 chr21_28022802_28023902:569 T C 101 69 20 True
IISNP66 chr17_80531082_80532207 501 626 rs4789798 chr17_80531082_80532207:562 C G 126 62 45 True
IISNP67 chr17_6810940_6812066 501 627 rs4796362 chr17_6810940_6812066:590 G A 127 90 46 False
IISNP68 chr1_105717077_105718184 501 608 rs4847034 chr1_105717077_105718184:555 A G 108 55 27 True
IISNP69 chr18_47370442_47371541 501 600 rs521861 chr18_47370442_47371541:573 C G 100 73 19 True
IISNP7 chr13_100037637_100038761 501 625 rs1058083 chr13_100037637_100038761:597 A G 125 97 44 False
IISNP70 chr22_19920061_19921192 501 632 rs5746846 chr22_19920061_19921192:586 C G 132 86 51 False
IISNP71 chr11_122195414_122196543 501 630 rs590162 chr11_122195414_122196543:576 C T 130 76 49 True
IISNP72 chr3_193206814_193207921 501 608 rs6444724 chr3_193206814_193207921:567 T C 108 67 27 True
IISNP73 chr11_105912429_105913529 501 601 rs6591147 chr11_105912429_105913529:556 T C 101 56 20 True
IISNP74 chr17_80715140_80716246 501 607 rs689512 chr17_80715140_80716246:563 G C 107 63 26 True
IISNP75 chr16_7519685_7520809 501 625 rs7205345 chr16_7519685_7520809:570 C G 125 70 44 True
IISNP76 chr14_53216148_53217276 501 629 rs722290 chr14_53216148_53217276:576 G C 129 76 48 True
IISNP77 chr18_22738427_22739556 501 630 rs7229946 chr18_22738427_22739556:575 G A 130 75 49 True
IISNP78 chr10_118506324_118507433 501 610 rs740598 chr10_118506324_118507433:576 G A 110 76 29 True
IISNP79 chr1_14154833_14155962 501 630 rs7520386 chr1_14154833_14155962:570 G A 130 70 49 True
IISNP8 chr21_43606463_43607573 501 611 rs221956 chr21_43606463_43607573:535 T C 111 35 30 True
IISNP80 chr5_159487382_159488507 501 626 rs7704770 chr5_159487382_159488507:572 G A 126 72 45 True
IISNP81 chr17_41341424_41342523 501 600 rs8070085 chr17_41341424_41342523:561 A G 100 61 19 True
IISNP82 chr17_80461344_80462465 501 622 rs8078417 chr17_80461344_80462465:592 C T 122 92 41 False
IISNP83 chr1_239881353_239882471 501 619 rs891700 chr1_239881353_239882471:574 A G 119 74 38 True
IISNP84 chr11_11095660_11096769 501 610 rs901398 chr11_11095660_11096769:562 C T 110 62 29 True
IISNP85 chr13_84456181_84457286 501 606 rs9546538 chr13_84456181_84457286:555 T C 106 55 25 True
IISNP86 chr22_19919790_19920889 501 600 rs9606186 chr22_19919790_19920889:570 C G 100 70 19 True
IISNP87 chr18_29310484_29311587 501 604 rs985492 chr18_29310484_29311587:551 G A 104 51 23 True
IISNP88 chr3_59487752_59488863 501 612 rs9866013 chr3_59487752_59488863:589 T C 112 89 31 False
IISNP89 chr22_33558944_33560052 501 609 rs987640 chr22_33558944_33560052:565 T A 109 65 28 True
IISNP9 chr5_136632784_136633892 501 609 rs13182883 chr5_136632784_136633892:555 G A 109 55 28 True
IISNP90 chr17_2918812_2919921 501 610 rs9905977 chr17_2918812_2919921:582 A G 110 82 29 True
IISNP91 chr2_124108634_124109748 501 615 rs993934 chr2_124108634_124109748:580 A G 115 80 34 True
IISNP92 chr18_9749309_9750416 501 608 rs9951171 chr18_9749309_9750416:571 G A 108 71 27 True
IISNP93 chr7_47924777_47925902 501 626 rs10274334 chr7_47924777_47925902:555 C G 126 55 45 True
IISNP94 chr19_57085220_57086327 501 608 rs10421285 chr19_57085220_57086327:550 G C 108 50 27 True
IISNP95 chr19_41938759_41939869 501 611 rs1043413 chr19_41938759_41939869:539 C G 111 39 30 True
IISNP96 chr1_19447280_19448406 501 627 rs1044010 chr1_19447280_19448406:564 C G 127 64 46 True
IISNP97 chr8_142203762_142204884 501 623 rs1045248 chr8_142203762_142204884:565 C G 123 65 42 True
IISNP98 chr14_31354504_31355624 501 621 rs1045644 chr14_31354504_31355624:593 C G 121 93 40 False
IISNP99 chr11_58318053_58319181 501 629 rs1047979 chr11_58318053_58319181:567 C G 129 67 48 True

282 rows × 11 columns

In [110]:
afreq_nans = all_SNP.ix[(all_SNP.SNPPASSQC) & (all_SNP.ADJUSTEDFREQUENCY.isnull())].index.unique()
In [114]:
print(list(sorted(afreq_nans)))
['17-a1-h1-b1', '18-a1-h1-b1', '19-a1-h1-b1', '20-a1-h1-b1', '21-a1-h1-b1', '22-a1-h1-b1', '23-a1-h1-b1', '24-a1-h1-b1', '25-a1-h1-b1', '26-a1-h1-b1', '27-a1-h1-b1', '28-a1-h1-b1', '29-a1-h1-b1', '30-a1-h1-b1', '31-a1-h1-b1', '32-a1-h1-b1', '878-879-01', '878-879-02', '878-879-03', '878-879-04', '878-879-05', '878-879-06', '878-879-07', '878-879-08', '878-879-09', '878-882-01', '878-882-02', '878-882-03', '878-882-04', '878-882-05', '878-882-06', '878-882-07', '878-882-08', '878-882-09', '878-890-01', '878-890-02', '878-890-03', '878-890-04', '878-890-05', '878-890-06', '878-890-07', '878-890-08', '878-890-09', 'A150521Aa', 'A150521Ab', 'A150521Ba', 'A150521Bb', 'A150521Ca', 'A150521Cb', 'A150521Da', 'A150521Db', 'A150522Ea', 'A150522Eb', 'A150529Fa', 'A150529Fb', 'A150529Fcd', 'AB07-52-38', 'AI96-92-01', 'AK22-50-91', 'AL62-25-54', 'AS41-44-54', 'AVBlank-Aug-20-15', 'AVBlank-Aug-21-15', 'AVBlank-Aug-26-15', 'AVBlank-Aug-28-15', 'AVBlank-Aug-31-15', 'AVBlank-Sep-15-15', 'AVBlank-Sep-16-15', 'AVBlank-Sep-17-15', 'AVBlank-Sep-18-15', 'AVBlank-Sep-4-15', 'AVBlank-Sep-9-15', 'AVBlank-c-Sep-3-15', 'AVHigh1-Aug-20-15', 'AVHigh1-Aug-21-15', 'AVHigh1-Aug-26-15', 'AVHigh1-Aug-28-15', 'AVHigh1-Aug-31-15', 'AVHigh1-Sep-15-15', 'AVHigh1-Sep-16-15', 'AVHigh1-Sep-17-15', 'AVHigh1-Sep-18-15', 'AVHigh1-Sep-4-15', 'AVHigh1-Sep-9-15', 'AVHigh1-c-Sep-3-15', 'AVHigh2-Aug-20-15', 'AVHigh2-Aug-21-15', 'AVHigh2-Aug-26-15', 'AVHigh2-Aug-28-15', 'AVHigh2-Aug-31-15', 'AVHigh2-Sep-15-15', 'AVHigh2-Sep-16-15', 'AVHigh2-Sep-17-15', 'AVHigh2-Sep-18-15', 'AVHigh2-Sep-4-15', 'AVHigh2-Sep-9-15', 'AVHigh2-c-Sep-3-15', 'AVLow1-Aug-20-15', 'AVLow1-Aug-21-15', 'AVLow1-Aug-26-15', 'AVLow1-Aug-28-15', 'AVLow1-Aug-31-15', 'AVLow1-Sep-15-15', 'AVLow1-Sep-16-15', 'AVLow1-Sep-17-15', 'AVLow1-Sep-18-15', 'AVLow1-Sep-4-15', 'AVLow1-Sep-9-15', 'AVLow1-c-Sep-3-15', 'AVLow2-Aug-20-15', 'AVLow2-Aug-21-15', 'AVLow2-Aug-26-15', 'AVLow2-Aug-28-15', 'AVLow2-Aug-31-15', 'AVLow2-Sep-15-15', 'AVLow2-Sep-16-15', 'AVLow2-Sep-18-15', 'AVLow2-Sep-4-15', 'AVLow2-Sep-9-15', 'AVLow2-c-Sep-3-15', 'AVStreck0001-Aug-20-15', 'AVStreck0001-Aug-21-15', 'AVStreck0001-Aug-26-15', 'AVStreck0001-Aug-28-15', 'AVStreck0001-Aug-31-15', 'AVStreck0001-Sep-18-15', 'Aa', 'Ab', 'BJ06-11-07', 'BM48-78-43', 'BN30-68-87', 'BP02-02-48', 'BT99-10-22', 'Ba', 'Bb', 'C4-5-5-1-Aug-13-15', 'C4-5-5-2-Aug-13-15', 'C4-5-5-3-Aug-13-15', 'C4-5-7-1-Aug-13-15', 'C4-5-7-2-Aug-13-15', 'C4-5-7-3-Aug-13-15', 'C4-5-9-1-Aug-13-15', 'C4-5-9-2-Aug-13-15', 'C4-5-9-3-Aug-13-15', 'C5-5-5-1-Aug-13-15', 'C5-5-5-2-Aug-13-15', 'C5-5-7-1-Aug-13-15', 'C5-5-7-2-Aug-13-15', 'C5-5-7-3-Aug-13-15', 'C5-5-9-1-Aug-13-15', 'C5-5-9-2-Aug-13-15', 'CA02-87-78', 'CA91-50-33', 'CI78-80-72', 'CO59-99-45', 'CX79-19-15', 'CY32-38-29', 'CY90-45-41', 'CY97-97-83', 'CZ06-72-39', 'Ca', 'DD67-88-05', 'DE45-89-82', 'DLS-2010824-a1-h1-b1', 'DLS-2012024-a1-h1-b1', 'DLS-2020824-a1-h1-b1', 'DLS-2030824-a1-h1-b1', 'DLS-2032024-a1-h1-b1', 'DLS-2040824-a1-h1-b1', 'DLS-2050824-a1-h1-b1', 'DLS-2052024-a1-h1-b1', 'DLS-2060824-a1-h1-b1', 'DLS-2070824-a1-h1-b1', 'DLS-2072024-a1-h1-b1', 'DLS-2080824-a1-h1-b1', 'DLS-2090824-a1-h1-b1', 'DLS-2092024-a1-h1-b1', 'DLS-2100824-a1-h1-b1', 'DLS-2110824-a1-h1-b1', 'DLS4-1-0-A1-a1-h1-b1', 'DLS4-1-0-A2-a1-h1-b1', 'DLS4-1-0-B1-a1-h1-b1', 'DLS4-1-0-B2-a1-h1-b1', 'DLS4-1-0-C1-a1-h1-b1', 'DLS4-1-0-C2-a1-h1-b1', 'DLS4-1-0-D1-a1-h1-b1', 'DLS4-1-0-D2-a1-h1-b1', 'DLS4-1-0-E1-a1-h1-b1', 'DLS4-1-0-E2-a1-h1-b1', 'DLS4-1-0p5-A1-a1-h1-b1', 'DLS4-1-0p5-A2-a1-h1-b1', 'DLS4-1-0p5-B1-a1-h1-b1', 'DLS4-1-0p5-B2-a1-h1-b1', 'DLS4-1-0p5-C1-a1-h1-b1', 'DLS4-1-0p5-C2-a1-h1-b1', 'DLS4-1-0p5-C3-a1-h1-b1', 'DLS4-1-0p5-D1-a1-h1-b1', 'DLS4-1-0p5-D2-a1-h1-b1', 'DLS4-1-0p5-D3-a1-h1-b1', 'DLS4-1-0p5-E1-a1-h1-b1', 'DLS4-1-0p5-E2-a1-h1-b1', 'DLS4-1-0p5-E3-a1-h1-b1', 'DLS4-1-1', 'DLS4-1-1-A1-a1-h1-b1', 'DLS4-1-1-A2-a1-h1-b1', 'DLS4-1-1-B1-a1-h1-b1', 'DLS4-1-1-B2-a1-h1-b1', 'DLS4-1-1-C1-a1-h1-b1', 'DLS4-1-1-C2-a1-h1-b1', 'DLS4-1-1-D1-a1-h1-b1', 'DLS4-1-1-D2-a1-h1-b1', 'DLS4-1-1-E1-a1-h1-b1', 'DLS4-1-1-E2-a1-h1-b1', 'DLS4-1-100', 'DLS4-1-100-A1-a1-h1-b1', 'DLS4-1-100-A2-a1-h1-b1', 'DLS4-1-100-B1-a1-h1-b1', 'DLS4-1-100-B2-a1-h1-b1', 'DLS4-1-100-C1-a1-h1-b1', 'DLS4-1-100-C2-a1-h1-b1', 'DLS4-1-100-D1-a1-h1-b1', 'DLS4-1-100-D2-a1-h1-b1', 'DLS4-1-100-E1-a1-h1-b1', 'DLS4-1-100-E2-a1-h1-b1', 'DLS4-1-3-A1-a1-h1-b1', 'DLS4-1-3-A2-a1-h1-b1', 'DLS4-1-3-B1-a1-h1-b1', 'DLS4-1-3-B2-a1-h1-b1', 'DLS4-1-3-C1-a1-h1-b1', 'DLS4-1-3-C2-a1-h1-b1', 'DLS4-1-3-C3-a1-h1-b1', 'DLS4-1-3-D1-a1-h1-b1', 'DLS4-1-3-D2-a1-h1-b1', 'DLS4-1-3-D3-a1-h1-b1', 'DLS4-1-3-E1-a1-h1-b1', 'DLS4-1-3-E2-a1-h1-b1', 'DLS4-1-3-E3-a1-h1-b1', 'DLS4-2-0-B1-a1-h1-b1', 'DLS4-2-0-C1-a1-h1-b1', 'DLS4-2-0-D1-a1-h1-b1', 'DLS4-2-0-E1-a1-h1-b1', 'DLS4-2-0p5-B1-a1-h1-b1', 'DLS4-2-0p5-C1-a1-h1-b1', 'DLS4-2-0p5-D1-a1-h1-b1', 'DLS4-2-0p5-E1-a1-h1-b1', 'DLS4-2-100-B1-a1-h1-b1', 'DLS4-2-3-B1-a1-h1-b1', 'DV34-91-66', 'DX42-81-71', 'DX45-46-01', 'Da', 'EG35-12-76', 'EL30-36-39', 'EQ67-17-22', 'ES05-71-07', 'EX69-26-00', 'Ea', 'Eb', 'FG78-35-13', 'FL75-72-86', 'FN44-92-67', 'FR49-24-67', 'FR65-60-84', 'FT60-19-49', 'FT95-21-33', 'FZ88-59-94', 'Fa', 'Fb', 'GB61-23-72', 'GG40-39-07', 'GG99-38-50', 'GN50-37-27', 'GN55-85-68', 'GQ81-80-24', 'GZ96-86-33', 'Ga', 'HC87-23-78', 'HD-418-01-a1-h1-b1', 'HD-418-02-a1-h1-b1', 'HD-418-03-a1-h1-b1', 'HD-418-04-a1-h1-b1', 'HD-418-05-a1-h1-b1', 'HD-418-06-a1-h1-b1', 'HD-418-07-a1-h1-b1', 'HD-418-08-a1-h1-b1', 'HD-418-09-a1-h1-b1', 'HD-418-10-a1-h1-b1', 'HD-418-11-a1-h1-b1', 'HD-418-12-a1-h1-b1', 'HD-418-13-a1-h1-b1', 'HD-418-14-a1-h1-b1', 'HD-418-15-a1-h1-b1', 'HD-418-16-a1-h1-b1', 'HD-441-02-a1-h1-b1', 'HD-441-03-a1-h1-b1', 'HD-441-04-a1-h1-b1', 'HD-441-05-a1-h1-b1', 'HD-441-06-a1-h1-b1', 'HD-441-07-a1-h1-b1', 'HD-441-08-a1-h1-b1', 'HD-441-09-a1-h1-b1', 'HD-441-10-a1-h1-b1', 'HD-441-11-a1-h1-b1', 'HD-441-12-a1-h1-b1', 'HD-441-13-a1-h1-b1', 'HD-441-14-a1-h1-b1', 'HD-441-15-a1-h1-b1', 'HD-441-16-a1-h1-b1', 'HD-441-17-a1-h1-b1', 'HH45-40-34', 'HP51-95-01', 'HRZ-3-5-a1-h1-b1', 'HRZ-3-7-a1-h1-b1', 'HRZ-5-1-F1-a1-h1-b1', 'HRZ-5-1-F2-a1-h1-b1', 'HRZ-5-1-G1-a1-h1-b1', 'HRZ-5-1-G2-a1-h1-b1', 'HRZ-5-1-H1-a1-h1-b1', 'HRZ-5-1-H2-a1-h1-b1', 'HRZ-5-1-I1-a1-h1-b1', 'HRZ-5-1-I2-a1-h1-b1', 'HRZ-5-1-J1-a1-h1-b1', 'HRZ-5-1-J2-a1-h1-b1', 'HRZ-5-2-F2-a1-h1-b1', 'HRZ-5-2-G2-a1-h1-b1', 'HRZ-5-2-H2-a1-h1-b1', 'HRZ-5-2-I2-a1-h1-b1', 'HRZ-5-2-J2-a1-h1-b1', 'HRZ-5-4-F2-a1-h1-b1', 'HRZ-5-4-G2-a1-h1-b1', 'HRZ-5-4-H2-a1-h1-b1', 'HRZ-5-4-I2-a1-h1-b1', 'HRZ-5-4-J2-a1-h1-b1', 'HRZ-5-6-F2-a1-h1-b1', 'HRZ-5-6-G2-a1-h1-b1', 'HRZ-5-6-H2-a1-h1-b1', 'HRZ-5-6-I2-a1-h1-b1', 'HRZ-5-6-J2-a1-h1-b1', 'HRZ-6-3-O1-a1-h1-b1', 'HRZ-6-6-M1-a1-h1-b1', 'HRZ-6-6-N1-a1-h1-b1', 'HRZ-6-6-O1-a1-h1-b1', 'HRZ-601-03-27', 'HRZ-601-03-28', 'HRZ-601-03-29', 'HRZ-601-08-27', 'HRZ-601-08-28', 'HRZ-601-08-29', 'HRZ-602-03-26', 'HRZ-602-03-27', 'HRZ-602-03-28', 'HRZ-602-03-29', 'HRZ-602-08-26', 'HRZ-602-08-27', 'HRZ-602-08-28', 'HRZ-602-08-29', 'HRZ-603-03-26', 'HRZ-603-03-27', 'HRZ-603-03-28', 'HRZ-603-03-29', 'HRZ-603-08-26', 'HRZ-603-08-27', 'HRZ-603-08-28', 'HRZ-603-08-29', 'HRZ-604-03-26', 'HRZ-604-03-27', 'HRZ-604-03-28', 'HRZ-604-03-29', 'HRZ-604-08-26', 'HRZ-604-08-27', 'HRZ-604-08-28', 'HRZ-604-08-29', 'HRZ-605-03-26', 'HRZ-605-03-27', 'HRZ-605-03-28', 'HRZ-605-03-29', 'HRZ-605-08-26', 'HRZ-605-08-27', 'HRZ-605-08-28', 'HRZ-605-08-29', 'HRZ-606-03-26', 'HRZ-606-03-27', 'HRZ-606-03-28', 'HRZ-606-03-29', 'HRZ-606-08-26', 'HRZ-606-08-27', 'HRZ-606-08-28', 'HRZ-606-08-29', 'HRZ-607-03-26', 'HRZ-607-03-27', 'HRZ-607-03-28', 'HRZ-607-03-29', 'HRZ-607-08-26', 'HRZ-607-08-27', 'HRZ-607-08-28', 'HRZ-607-08-29', 'HRZ-608-03-26', 'HRZ-608-03-27', 'HRZ-608-03-28', 'HRZ-608-03-29', 'HRZ-608-08-26', 'HRZ-608-08-27', 'HRZ-608-08-28', 'HRZ-608-08-29', 'HRZ-609-03-26', 'HRZ-609-03-28', 'HRZ-609-03-29', 'HRZ-609-08-26', 'HRZ-609-08-28', 'HRZ-609-08-29', 'HRZ-7-1-a', 'HRZ-7-3-M1-a1-h1-b1', 'HRZ-7-3-N1-a1-h1-b1', 'HRZ-7-3-O1-a1-h1-b1', 'HRZ-7-3-a', 'HRZ-7-6-M1-a1-h1-b1', 'HRZ-7-6-N1-a1-h1-b1', 'HRZ-7-6-O1-a1-h1-b1', 'HRZ-7-6-a', 'HRZ-701-03-26', 'HRZ-701-03-27', 'HRZ-701-03-29', 'HRZ-701-08-26', 'HRZ-701-08-27', 'HRZ-701-08-29', 'HRZ-702-03-26', 'HRZ-702-03-27', 'HRZ-702-03-28', 'HRZ-702-03-29', 'HRZ-702-08-26', 'HRZ-702-08-27', 'HRZ-702-08-28', 'HRZ-702-08-29', 'HRZ-703-03-26', 'HRZ-703-03-27', 'HRZ-703-03-28', 'HRZ-703-03-29', 'HRZ-703-08-26', 'HRZ-703-08-27', 'HRZ-703-08-28', 'HRZ-703-08-29', 'HRZ-704-03-26', 'HRZ-704-03-27', 'HRZ-704-03-28', 'HRZ-704-03-29', 'HRZ-704-08-26', 'HRZ-704-08-27', 'HRZ-704-08-28', 'HRZ-704-08-29', 'HRZ-705-03-26', 'HRZ-705-03-27', 'HRZ-705-03-28', 'HRZ-705-03-29', 'HRZ-705-08-26', 'HRZ-705-08-27', 'HRZ-705-08-28', 'HRZ-705-08-29', 'HRZ-706-03-26', 'HRZ-706-03-27', 'HRZ-706-03-28', 'HRZ-706-03-29', 'HRZ-706-08-26', 'HRZ-706-08-27', 'HRZ-706-08-28', 'HRZ-706-08-29', 'HRZ-707-03-26', 'HRZ-707-03-27', 'HRZ-707-03-28', 'HRZ-707-03-29', 'HRZ-707-08-26', 'HRZ-707-08-27', 'HRZ-707-08-28', 'HRZ-707-08-29', 'HRZ-708-03-26', 'HRZ-708-03-27', 'HRZ-708-03-28', 'HRZ-708-03-29', 'HRZ-708-08-26', 'HRZ-708-08-27', 'HRZ-708-08-29', 'HRZ-8-3-M1-a1-h1-b1', 'HRZ-8-3-N1-a1-h1-b1', 'HRZ-8-3-O1-a1-h1-b1', 'HRZ-8-6-M1-a1-h1-b1', 'HRZ-8-6-N1-a1-h1-b1', 'HRZ-8-6-O1-a1-h1-b1', 'HRZ-801-03-26', 'HRZ-801-03-27', 'HRZ-801-03-28', 'HRZ-801-08-26', 'HRZ-801-08-27', 'HRZ-801-08-28', 'HRZ-801A-00-1', 'HRZ-801A-00-2', 'HRZ-801A-05-1', 'HRZ-801A-05-2', 'HRZ-801A-10-1', 'HRZ-801A-10-2', 'HRZ-801A-30-1', 'HRZ-801A-30-2', 'HRZ-802-03-26', 'HRZ-802-03-27', 'HRZ-802-03-28', 'HRZ-802-03-29', 'HRZ-802-08-26', 'HRZ-802-08-27', 'HRZ-802-08-28', 'HRZ-802-08-29', 'HRZ-803-03-26', 'HRZ-803-03-27', 'HRZ-803-03-28', 'HRZ-803-03-29', 'HRZ-803-08-26', 'HRZ-803-08-27', 'HRZ-803-08-28', 'HRZ-803-08-29', 'HRZ-804-03-26', 'HRZ-804-03-27', 'HRZ-804-03-28', 'HRZ-804-03-29', 'HRZ-804-08-26', 'HRZ-804-08-27', 'HRZ-804-08-28', 'HRZ-804-08-29', 'HRZ-805-03-26', 'HRZ-805-03-27', 'HRZ-805-03-28', 'HRZ-805-03-29', 'HRZ-805-08-26', 'HRZ-805-08-27', 'HRZ-805-08-28', 'HRZ-805-08-29', 'HRZ-806-03-26', 'HRZ-806-03-27', 'HRZ-806-03-28', 'HRZ-806-03-29', 'HRZ-806-08-26', 'HRZ-806-08-27', 'HRZ-806-08-28', 'HRZ-806-08-29', 'HRZ-807-03-26', 'HRZ-807-03-27', 'HRZ-807-03-28', 'HRZ-807-03-29', 'HRZ-807-08-26', 'HRZ-807-08-27', 'HRZ-807-08-28', 'HRZ-807-08-29', 'HRZ-808-03-26', 'HRZ-808-03-27', 'HRZ-808-03-28', 'HRZ-808-03-29', 'HRZ-808-08-26', 'HRZ-808-08-27', 'HRZ-808-08-28', 'HRZ-808-08-29', 'HRZ-8a-1-0-a', 'HRZ-8a-1-0-b', 'HRZ-8a-1-1-a', 'HRZ-8a-1-1-b', 'HRZ-8a-1-3-a', 'HRZ-8a-1-3-b', 'HRZ-8a-105-a', 'HRZ-8a-105-b', 'HRZ-cntrl-1', 'HRZ-cntrl-3', 'HRZ0060203-Aug-20-15', 'HRZ0060203-Aug-21-15', 'HRZ0060203-Aug-26-15', 'HRZ0060203-Aug-28-15', 'HRZ0060203-Aug-31-15', 'HRZ0060203-Sep-15-15', 'HRZ0060203-Sep-16-15', 'HRZ0060203-Sep-17-15', 'HRZ0060203-Sep-18-15', 'HRZ0060203-Sep-4-15', 'HRZ0060203-Sep-9-15', 'HRZ0060203-c-Sep-3-15', 'HRZ0060208-Aug-20-15', 'HRZ0060208-Aug-21-15', 'HRZ0060208-Aug-26-15', 'HRZ0060208-Aug-28-15', 'HRZ0060208-Aug-31-15', 'HRZ0060208-Sep-15-15', 'HRZ0060208-Sep-16-15', 'HRZ0060208-Sep-17-15', 'HRZ0060208-Sep-18-15', 'HRZ0060208-Sep-4-15', 'HRZ0060208-Sep-9-15', 'HRZ0060208-c-Sep-3-15', 'HRZ0060303-Aug-20-15', 'HRZ0060303-Aug-21-15', 'HRZ0060303-Aug-26-15', 'HRZ0060303-Aug-28-15', 'HRZ0060303-Aug-31-15', 'HRZ0060303-Sep-15-15', 'HRZ0060303-Sep-16-15', 'HRZ0060303-Sep-17-15', 'HRZ0060303-Sep-18-15', 'HRZ0060303-Sep-4-15', 'HRZ0060303-Sep-9-15', 'HRZ0060303-c-Sep-3-15', 'HRZ0060308-Aug-20-15', 'HRZ0060308-Aug-21-15', 'HRZ0060308-Aug-26-15', 'HRZ0060308-Aug-28-15', 'HRZ0060308-Aug-31-15', 'HRZ0060308-Sep-15-15', 'HRZ0060308-Sep-16-15', 'HRZ0060308-Sep-17-15', 'HRZ0060308-Sep-18-15', 'HRZ0060308-Sep-4-15', 'HRZ0060308-Sep-9-15', 'HRZ0060308-c-Sep-3-15', 'HRZ0060403-Aug-20-15', 'HRZ0060403-Aug-21-15', 'HRZ0060403-Aug-26-15', 'HRZ0060403-Aug-28-15', 'HRZ0060403-Aug-31-15', 'HRZ0060403-Sep-15-15', 'HRZ0060403-Sep-16-15', 'HRZ0060403-Sep-17-15', 'HRZ0060403-Sep-18-15', 'HRZ0060403-Sep-4-15', 'HRZ0060403-Sep-9-15', 'HRZ0060403-c-Sep-3-15', 'HRZ0060408-Aug-20-15', 'HRZ0060408-Aug-21-15', 'HRZ0060408-Aug-26-15', 'HRZ0060408-Aug-28-15', 'HRZ0060408-Aug-31-15', 'HRZ0060408-Sep-15-15', 'HRZ0060408-Sep-16-15', 'HRZ0060408-Sep-17-15', 'HRZ0060408-Sep-18-15', 'HRZ0060408-Sep-4-15', 'HRZ0060408-Sep-9-15', 'HRZ0060408-c-Sep-3-15', 'HRZ0060503-Aug-20-15', 'HRZ0060503-Aug-21-15', 'HRZ0060503-Aug-26-15', 'HRZ0060503-Aug-28-15', 'HRZ0060503-Aug-31-15', 'HRZ0060503-Sep-15-15', 'HRZ0060503-Sep-16-15', 'HRZ0060503-Sep-17-15', 'HRZ0060503-Sep-18-15', 'HRZ0060503-Sep-4-15', 'HRZ0060503-Sep-9-15', 'HRZ0060503-c-Sep-3-15', 'HRZ0060508-Aug-20-15', 'HRZ0060508-Aug-21-15', 'HRZ0060508-Aug-26-15', 'HRZ0060508-Aug-28-15', 'HRZ0060508-Aug-31-15', 'HRZ0060508-Sep-15-15', 'HRZ0060508-Sep-16-15', 'HRZ0060508-Sep-18-15', 'HRZ0060508-Sep-4-15', 'HRZ0060508-Sep-9-15', 'HRZ0060508-c-Sep-3-15', 'HRZ0060603-Aug-20-15', 'HRZ0060603-Aug-21-15', 'HRZ0060603-Aug-26-15', 'HRZ0060603-Aug-28-15', 'HRZ0060603-Aug-31-15', 'HRZ0060603-Sep-15-15', 'HRZ0060603-Sep-16-15', 'HRZ0060603-Sep-17-15', 'HRZ0060603-Sep-18-15', 'HRZ0060603-Sep-4-15', 'HRZ0060603-Sep-9-15', 'HRZ0060603-c-Sep-3-15', 'HRZ0060608-Aug-20-15', 'HRZ0060608-Aug-21-15', 'HRZ0060608-Aug-26-15', 'HRZ0060608-Aug-28-15', 'HRZ0060608-Aug-31-15', 'HRZ0060608-Sep-15-15', 'HRZ0060608-Sep-16-15', 'HRZ0060608-Sep-17-15', 'HRZ0060608-Sep-18-15', 'HRZ0060608-Sep-4-15', 'HRZ0060608-Sep-9-15', 'HRZ0060608-c-Sep-3-15', 'HRZ0060703-Aug-20-15', 'HRZ0060703-Aug-21-15', 'HRZ0060703-Aug-26-15', 'HRZ0060703-Aug-28-15', 'HRZ0060703-Aug-31-15', 'HRZ0060703-Sep-15-15', 'HRZ0060703-Sep-16-15', 'HRZ0060703-Sep-17-15', 'HRZ0060703-Sep-18-15', 'HRZ0060703-Sep-4-15', 'HRZ0060703-Sep-9-15', 'HRZ0060703-c-Sep-3-15', 'HRZ0060708-Aug-20-15', 'HRZ0060708-Aug-21-15', 'HRZ0060708-Aug-26-15', 'HRZ0060708-Aug-28-15', 'HRZ0060708-Aug-31-15', 'HRZ0060708-Sep-15-15', 'HRZ0060708-Sep-16-15', 'HRZ0060708-Sep-17-15', 'HRZ0060708-Sep-18-15', 'HRZ0060708-Sep-4-15', 'HRZ0060708-Sep-9-15', 'HRZ0060803-Aug-20-15', 'HRZ0060803-Aug-21-15', 'HRZ0060803-Aug-26-15', 'HRZ0060803-Aug-28-15', 'HRZ0060803-Aug-31-15', 'HRZ0060803-Sep-15-15', 'HRZ0060803-Sep-16-15', 'HRZ0060803-Sep-17-15', 'HRZ0060803-Sep-18-15', 'HRZ0060803-Sep-4-15', 'HRZ0060803-Sep-9-15', 'HRZ0060803-c-Sep-3-15', 'HRZ0060808-Aug-20-15', 'HRZ0060808-Aug-21-15', 'HRZ0060808-Aug-26-15', 'HRZ0060808-Aug-28-15', 'HRZ0060808-Aug-31-15', 'HRZ0060808-Sep-15-15', 'HRZ0060808-Sep-16-15', 'HRZ0060808-Sep-17-15', 'HRZ0060808-Sep-18-15', 'HRZ0060808-Sep-4-15', 'HRZ0060808-Sep-9-15', 'HRZ0060808-c-Sep-3-15', 'HRZ0070203-Aug-20-15', 'HRZ0070203-Aug-21-15', 'HRZ0070203-Aug-26-15', 'HRZ0070203-Aug-28-15', 'HRZ0070203-Aug-31-15', 'HRZ0070203-Sep-15-15', 'HRZ0070203-Sep-16-15', 'HRZ0070203-Sep-17-15', 'HRZ0070203-Sep-18-15', 'HRZ0070203-Sep-4-15', 'HRZ0070203-Sep-9-15', 'HRZ0070203-c-Sep-3-15', 'HRZ0070208-Aug-20-15', 'HRZ0070208-Aug-21-15', 'HRZ0070208-Aug-26-15', 'HRZ0070208-Aug-28-15', 'HRZ0070208-Aug-31-15', 'HRZ0070208-Sep-15-15', 'HRZ0070208-Sep-16-15', 'HRZ0070208-Sep-17-15', 'HRZ0070208-Sep-18-15', 'HRZ0070208-Sep-4-15', 'HRZ0070208-Sep-9-15', 'HRZ0070208-c-Sep-3-15', 'HRZ0070303-Aug-20-15', 'HRZ0070303-Aug-21-15', 'HRZ0070303-Aug-26-15', 'HRZ0070303-Aug-28-15', 'HRZ0070303-Aug-31-15', 'HRZ0070303-Sep-15-15', 'HRZ0070303-Sep-16-15', 'HRZ0070303-Sep-17-15', 'HRZ0070303-Sep-18-15', 'HRZ0070303-Sep-4-15', 'HRZ0070303-Sep-9-15', 'HRZ0070303-c-Sep-3-15', 'HRZ0070308-Aug-20-15', 'HRZ0070308-Aug-21-15', 'HRZ0070308-Aug-26-15', 'HRZ0070308-Aug-28-15', 'HRZ0070308-Aug-31-15', 'HRZ0070308-Sep-15-15', 'HRZ0070308-Sep-16-15', 'HRZ0070308-Sep-17-15', 'HRZ0070308-Sep-18-15', 'HRZ0070308-Sep-4-15', 'HRZ0070308-Sep-9-15', 'HRZ0070308-c-Sep-3-15', 'HRZ0070403-Aug-20-15', 'HRZ0070403-Aug-21-15', 'HRZ0070403-Aug-26-15', 'HRZ0070403-Aug-28-15', 'HRZ0070403-Aug-31-15', 'HRZ0070403-Sep-15-15', 'HRZ0070403-Sep-16-15', 'HRZ0070403-Sep-17-15', 'HRZ0070403-Sep-18-15', 'HRZ0070403-Sep-4-15', 'HRZ0070403-Sep-9-15', 'HRZ0070403-c-Sep-3-15', 'HRZ0070408-Aug-20-15', 'HRZ0070408-Aug-21-15', 'HRZ0070408-Aug-26-15', 'HRZ0070408-Aug-28-15', 'HRZ0070408-Aug-31-15', 'HRZ0070408-Sep-15-15', 'HRZ0070408-Sep-16-15', 'HRZ0070408-Sep-17-15', 'HRZ0070408-Sep-18-15', 'HRZ0070408-Sep-4-15', 'HRZ0070408-Sep-9-15', 'HRZ0070408-c-Sep-3-15', 'HRZ0070503-Aug-20-15', 'HRZ0070503-Aug-21-15', 'HRZ0070503-Aug-26-15', 'HRZ0070503-Aug-28-15', 'HRZ0070503-Aug-31-15', 'HRZ0070503-Sep-15-15', 'HRZ0070503-Sep-16-15', 'HRZ0070503-Sep-17-15', 'HRZ0070503-Sep-18-15', 'HRZ0070503-Sep-4-15', 'HRZ0070503-Sep-9-15', 'HRZ0070503-c-Sep-3-15', 'HRZ0070508-Aug-20-15', 'HRZ0070508-Aug-21-15', 'HRZ0070508-Aug-26-15', 'HRZ0070508-Aug-28-15', 'HRZ0070508-Aug-31-15', 'HRZ0070508-Sep-15-15', 'HRZ0070508-Sep-16-15', 'HRZ0070508-Sep-17-15', 'HRZ0070508-Sep-18-15', 'HRZ0070508-Sep-4-15', 'HRZ0070508-Sep-9-15', 'HRZ0070508-c-Sep-3-15', 'HRZ0070603-Aug-20-15', 'HRZ0070603-Aug-21-15', 'HRZ0070603-Aug-26-15', 'HRZ0070603-Aug-28-15', 'HRZ0070603-Aug-31-15', 'HRZ0070603-Sep-15-15', 'HRZ0070603-Sep-16-15', 'HRZ0070603-Sep-17-15', 'HRZ0070603-Sep-18-15', 'HRZ0070603-Sep-4-15', 'HRZ0070603-Sep-9-15', 'HRZ0070603-c-Sep-3-15', 'HRZ0070608-Aug-20-15', 'HRZ0070608-Aug-21-15', 'HRZ0070608-Aug-26-15', 'HRZ0070608-Aug-28-15', 'HRZ0070608-Aug-31-15', 'HRZ0070608-Sep-15-15', 'HRZ0070608-Sep-16-15', 'HRZ0070608-Sep-17-15', 'HRZ0070608-Sep-18-15', 'HRZ0070608-Sep-4-15', 'HRZ0070608-Sep-9-15', 'HRZ0070608-c-Sep-3-15', 'HRZ0070703-Aug-20-15', 'HRZ0070703-Aug-21-15', 'HRZ0070703-Aug-26-15', 'HRZ0070703-Aug-28-15', 'HRZ0070703-Aug-31-15', 'HRZ0070703-Sep-15-15', 'HRZ0070703-Sep-16-15', 'HRZ0070703-Sep-17-15', 'HRZ0070703-Sep-18-15', 'HRZ0070703-Sep-4-15', 'HRZ0070703-Sep-9-15', 'HRZ0070703-c-Sep-3-15', 'HRZ0070708-Aug-20-15', 'HRZ0070708-Aug-21-15', 'HRZ0070708-Aug-26-15', 'HRZ0070708-Aug-28-15', 'HRZ0070708-Aug-31-15', 'HRZ0070708-Sep-15-15', 'HRZ0070708-Sep-16-15', 'HRZ0070708-Sep-17-15', 'HRZ0070708-Sep-18-15', 'HRZ0070708-Sep-4-15', 'HRZ0070708-Sep-9-15', 'HRZ0070708-c-Sep-3-15', 'HRZ0070803-Aug-20-15', 'HRZ0070803-Aug-21-15', 'HRZ0070803-Aug-26-15', 'HRZ0070803-Aug-28-15', 'HRZ0070803-Aug-31-15', 'HRZ0070803-Sep-15-15', 'HRZ0070803-Sep-16-15', 'HRZ0070803-Sep-17-15', 'HRZ0070803-Sep-18-15', 'HRZ0070803-Sep-4-15', 'HRZ0070803-Sep-9-15', 'HRZ0070803-c-Sep-3-15', 'HRZ0070808-Aug-20-15', 'HRZ0070808-Aug-21-15', 'HRZ0070808-Aug-26-15', 'HRZ0070808-Aug-28-15', 'HRZ0070808-Aug-31-15', 'HRZ0070808-Sep-15-15', 'HRZ0070808-Sep-16-15', 'HRZ0070808-Sep-17-15', 'HRZ0070808-Sep-18-15', 'HRZ0070808-Sep-4-15', 'HRZ0070808-Sep-9-15', 'HRZ0070808-c-Sep-3-15', 'HRZ0080203-Aug-20-15', 'HRZ0080203-Aug-21-15', 'HRZ0080203-Aug-26-15', 'HRZ0080203-Aug-28-15', 'HRZ0080203-Aug-31-15', 'HRZ0080203-Sep-15-15', 'HRZ0080203-Sep-16-15', 'HRZ0080203-Sep-17-15', 'HRZ0080203-Sep-18-15', 'HRZ0080203-Sep-4-15', 'HRZ0080203-Sep-9-15', 'HRZ0080203-c-Sep-3-15', 'HRZ0080208-Aug-20-15', 'HRZ0080208-Aug-21-15', 'HRZ0080208-Aug-26-15', 'HRZ0080208-Aug-28-15', 'HRZ0080208-Aug-31-15', 'HRZ0080208-Sep-15-15', 'HRZ0080208-Sep-16-15', 'HRZ0080208-Sep-17-15', 'HRZ0080208-Sep-18-15', 'HRZ0080208-Sep-4-15', 'HRZ0080208-Sep-9-15', 'HRZ0080208-c-Sep-3-15', 'HRZ0080303-Aug-20-15', 'HRZ0080303-Aug-21-15', 'HRZ0080303-Aug-26-15', 'HRZ0080303-Aug-28-15', 'HRZ0080303-Aug-31-15', 'HRZ0080303-Sep-15-15', 'HRZ0080303-Sep-16-15', 'HRZ0080303-Sep-17-15', 'HRZ0080303-Sep-18-15', 'HRZ0080303-Sep-4-15', 'HRZ0080303-Sep-9-15', 'HRZ0080303-c-Sep-3-15', 'HRZ0080308-Aug-20-15', 'HRZ0080308-Aug-21-15', 'HRZ0080308-Aug-26-15', 'HRZ0080308-Aug-28-15', 'HRZ0080308-Aug-31-15', 'HRZ0080308-Sep-15-15', 'HRZ0080308-Sep-16-15', 'HRZ0080308-Sep-17-15', 'HRZ0080308-Sep-18-15', 'HRZ0080308-Sep-4-15', 'HRZ0080308-Sep-9-15', 'HRZ0080308-c-Sep-3-15', 'HRZ0080403-Aug-20-15', 'HRZ0080403-Aug-21-15', 'HRZ0080403-Aug-26-15', 'HRZ0080403-Aug-28-15', 'HRZ0080403-Aug-31-15', 'HRZ0080403-Sep-15-15', 'HRZ0080403-Sep-16-15', 'HRZ0080403-Sep-17-15', 'HRZ0080403-Sep-18-15', 'HRZ0080403-Sep-4-15', 'HRZ0080403-Sep-9-15', 'HRZ0080403-c-Sep-3-15', 'HRZ0080408-Aug-20-15', 'HRZ0080408-Aug-21-15', 'HRZ0080408-Aug-26-15', 'HRZ0080408-Aug-28-15', 'HRZ0080408-Aug-31-15', 'HRZ0080408-Sep-15-15', 'HRZ0080408-Sep-16-15', 'HRZ0080408-Sep-17-15', 'HRZ0080408-Sep-18-15', 'HRZ0080408-Sep-4-15', 'HRZ0080408-Sep-9-15', 'HRZ0080408-c-Sep-3-15', 'HRZ0080503-Aug-20-15', 'HRZ0080503-Aug-21-15', 'HRZ0080503-Aug-26-15', 'HRZ0080503-Aug-28-15', 'HRZ0080503-Aug-31-15', 'HRZ0080503-Sep-15-15', 'HRZ0080503-Sep-16-15', 'HRZ0080503-Sep-17-15', 'HRZ0080503-Sep-18-15', 'HRZ0080503-Sep-4-15', 'HRZ0080503-Sep-9-15', 'HRZ0080503-c-Sep-3-15', 'HRZ0080508-Aug-20-15', 'HRZ0080508-Aug-21-15', 'HRZ0080508-Aug-26-15', 'HRZ0080508-Aug-28-15', 'HRZ0080508-Aug-31-15', 'HRZ0080508-Sep-15-15', 'HRZ0080508-Sep-16-15', 'HRZ0080508-Sep-17-15', 'HRZ0080508-Sep-18-15', 'HRZ0080508-Sep-4-15', 'HRZ0080508-Sep-9-15', 'HRZ0080508-c-Sep-3-15', 'HRZ0080603-Aug-20-15', 'HRZ0080603-Aug-21-15', 'HRZ0080603-Aug-26-15', 'HRZ0080603-Aug-28-15', 'HRZ0080603-Aug-31-15', 'HRZ0080603-Sep-15-15', 'HRZ0080603-Sep-16-15', 'HRZ0080603-Sep-17-15', 'HRZ0080603-Sep-18-15', 'HRZ0080603-Sep-4-15', 'HRZ0080603-Sep-9-15', 'HRZ0080603-c-Sep-3-15', 'HRZ0080608-Aug-20-15', 'HRZ0080608-Aug-21-15', 'HRZ0080608-Aug-26-15', 'HRZ0080608-Aug-28-15', 'HRZ0080608-Aug-31-15', 'HRZ0080608-Sep-15-15', 'HRZ0080608-Sep-16-15', 'HRZ0080608-Sep-17-15', 'HRZ0080608-Sep-18-15', 'HRZ0080608-Sep-4-15', 'HRZ0080608-Sep-9-15', 'HRZ0080608-c-Sep-3-15', 'HRZ0080703-Aug-20-15', 'HRZ0080703-Aug-21-15', 'HRZ0080703-Aug-26-15', 'HRZ0080703-Aug-28-15', 'HRZ0080703-Aug-31-15', 'HRZ0080703-Sep-15-15', 'HRZ0080703-Sep-16-15', 'HRZ0080703-Sep-17-15', 'HRZ0080703-Sep-18-15', 'HRZ0080703-Sep-4-15', 'HRZ0080703-Sep-9-15', 'HRZ0080703-c-Sep-3-15', 'HRZ0080708-Aug-20-15', 'HRZ0080708-Aug-21-15', 'HRZ0080708-Aug-26-15', 'HRZ0080708-Aug-28-15', 'HRZ0080708-Aug-31-15', 'HRZ0080708-Sep-15-15', 'HRZ0080708-Sep-16-15', 'HRZ0080708-Sep-17-15', 'HRZ0080708-Sep-18-15', 'HRZ0080708-Sep-4-15', 'HRZ0080708-Sep-9-15', 'HRZ0080708-c-Sep-3-15', 'HRZ0080803-Aug-20-15', 'HRZ0080803-Aug-21-15', 'HRZ0080803-Aug-26-15', 'HRZ0080803-Aug-28-15', 'HRZ0080803-Aug-31-15', 'HRZ0080803-Sep-15-15', 'HRZ0080803-Sep-16-15', 'HRZ0080803-Sep-17-15', 'HRZ0080803-Sep-18-15', 'HRZ0080803-Sep-4-15', 'HRZ0080803-Sep-9-15', 'HRZ0080803-c-Sep-3-15', 'HRZ0080808-Aug-20-15', 'HRZ0080808-Aug-21-15', 'HRZ0080808-Aug-26-15', 'HRZ0080808-Aug-28-15', 'HRZ0080808-Aug-31-15', 'HRZ0080808-Sep-15-15', 'HRZ0080808-Sep-16-15', 'HRZ0080808-Sep-17-15', 'HRZ0080808-Sep-18-15', 'HRZ0080808-Sep-4-15', 'HRZ0080808-Sep-9-15', 'HRZ0080808-c-Sep-3-15', 'HW08-06-83', 'IG50-21-31', 'IM90-62-42', 'IY97-58-23', 'JC-01-A', 'JC-01-B', 'JC-02-A', 'JC-02-B', 'JC-03-A', 'JC-03-B', 'JC-04-A', 'JC-04-B', 'JC-05', 'JC-06', 'JC-07', 'KG83-89-57', 'KV58-98-42', 'KX01-05-88', 'KX80-58-26', 'LD11-86-62', 'LJ72-06-68', 'LL20-60-86', 'LQ16-67-52', 'MA22-22-20', 'ME79-73-03', 'MF13-03-39', 'MI41-07-98', 'MP07-41-28', 'MP60-53-24', 'MW02-30-99', 'NA12878-01', 'NA12878-02', 'NA12879-01', 'NA12879-02', 'NA12882-01', 'NA12882-02', 'NA12890-01', 'NA12890-02', 'NE01-89-50', 'NHV-Q4-1', 'NHV-Q4-2', 'NHV-Q4-3', 'NHV-Q5-1', 'NHV-Q5-2', 'NHV-Q5-3', 'NHV-Q6-1', 'NHV-Q6-2', 'NHV-Q6-3', 'NI77-14-46', 'NIST', 'NJ39-19-29', 'NK96-09-10', 'NO56-89-30', 'NO95-83-22', 'NQ02-54-12', 'NQ80-95-73', 'OD79-34-69', 'OI11-03-15', 'OK43-50-43', 'OL19-92-31', 'OR60-37-19', 'OY30-67-72', 'PG00-90-14', 'PI92-98-79', 'PQ27-24-18', 'PQ56-06-86', 'PW97-59-48', 'QB93-89-00', 'QF20-58-40', 'RC76-05-11', 'RD31-53-29', 'RG69-02-63', 'RQ00-34-92', 'RT53-40-83', 'RX22-37-29', 'SF29-03-65', 'SG45-36-99', 'SS58-50-74', 'ST98-63-50', 'SU71-58-99', 'SX86-07-29', 'Streck0002-Sep-15-15', 'Streck0002-Sep-16-15', 'Streck0002-Sep-17-15', 'Streck0002-Sep-4-15', 'Streck0002-Sep-9-15', 'Streck0002-c-Sep-3-15', 'TD92-84-54', 'TG79-52-42', 'TN63-88-05', 'TY67-93-88', 'UI96-96-96', 'UJ43-08-54', 'UP11-02-86', 'US01-19-76', 'UW82-31-47', 'VB54-31-04', 'VB61-00-15', 'VG37-78-73', 'VJ95-82-66', 'VK18-09-72', 'VL73-74-59', 'VR89-80-02', 'VR99-08-16', 'VY36-96-32', 'WO44-13-06', 'WO64-26-85', 'WS04-26-25', 'WU16-76-81', 'WZ89-91-33', 'XE11-41-53', 'XI29-64-88', 'XK83-48-90', 'XQ71-96-42', 'XT12-13-13', 'XU28-26-81', 'XY76-78-25', 'YB79-06-28', 'YF53-87-14', 'YG15-25-68', 'YK13-41-23', 'YL80-02-83', 'YM64-86-39', 'YP06-22-79', 'YP77-91-57', 'YQ46-38-01', 'ZE80-53-92', 'ZG94-43-02', 'ZI89-88-24', 'ZK73-98-08', 'ZS29-63-16']
In [130]:
nans_exps = all_SNP[all_SNP.index.isin(afreq_nans)].EXPERIMENT_NAME.unique()
nans_exps
Out[130]:
array(['BC150616-Analytical-2Hawk', 'CC150608-Pool2',
       'CM150603-Analytical-Chip-pool1', 'CC150630-HF-pool1',
       'KT150701a-pool2-Hawk', 'KT150701a-pool1-BigBird',
       'KT150701b-pool3', 'CM150701-Analytical-Chip-pool1',
       'KT150701b-pool2', 'BC150623-Analytical-2Falcon',
       'BC150603-Analytical-1BigBird', 'KT150716a-pool1-BB', 'Pazitpool1',
       'KT150716a-pool3-H', 'BC150803-Analytical-Chip28-3BigBird',
       'BC150803-Analytical-Chip29-1Falcon', 'KT150701b-pool1-BB',
       'Pazitpool3', 'BC150803-Analytical-Chip29-2Hawk',
       'BC150803-Analytical-Chip29-3Osprey',
       'BC150803-Analytical-Chip25-3Hawk',
       'BC150803-Analytical-Chip25-1BigBird',
       'BC150803-Analytical-Chip25-2Falcon', 'Pazitpool2', 'CCPool3',
       'CorinaTestRunPool2', 'CorinaTestRunPool3', 'CDC26AugPool2',
       'CDC26AugPool3', 'CM150804-Analytical-Chip-pool1',
       'CM150804-Analytical-Chip-pool2', 'CM150804-Analytical-Chip-pool5',
       'CM150804-Analytical-Chip-pool4', 'CM150804-Analytical-Chip-pool3',
       'PQ-CC2', 'BC150803-Analytical-Chip27-2BigBird',
       'BC150803-Analytical-Chip27-1Osprey',
       'BC150803-Analytical-Chip27-3Falcon', 'CorinaTestRun',
       'BC150803-Analytical-Chip21-1Hawk', 'BC150812-repool-F',
       'BC150803-Analytical-Chip21-2Osprey', 'CCPool2', 'CC2-Pool1',
       'CDC26AugPool1', 'CM31Aug2015Pool1', 'CM31Aug2015Pool2',
       'CM31Aug2015Pool3', 'CM1Sep2015Pool3', 'CM1Sep2015Pool2',
       'CM1Sep2015Pool1', 'CDC2Sep2015Pool2', 'CDC2Sep2015Pool3',
       'CDC8Sep2015Pool1', 'KT150831-pool1-BB', 'CDC8Sep2015Pool2',
       'CDC8Sep2015Pool3', 'CDC2Sep2015Pool1', 'KT150831-pool2-F',
       'KT150831-pool3-H', 'CYC11Sep2015Pool2', 'CYC11Sep2015Pool1',
       'BC150902-Chip30-16DOAR', 'BC150902-Chip30-ContamSmpls-Trovagene',
       'PS16SEP2015P3', 'PS16SEP2015P1', 'PS16SEP2015P2',
       'BC150902-Chip32-1BigBird', 'BC150902-Chip32-2BigBird',
       'CYC11Sep2015Pool3', 'PS02SEP2015P3', 'CYC04Sep2015Pool3',
       'CYC04Sep2015Pool2', 'PS02SEP2015P2', 'CYC04Sep2015Pool1',
       'JC150915-Pool1', 'PS02SEP2015P1', 'StanfordPedsChip3-pool3',
       'JC150915-Pool3', 'StanfordPedsChip1-pool3',
       'StanfordPedsChip5-pool3', 'StanfordPedsChip7-pool3',
       'StanfordPedsChip4-pool3', 'StanfordPedsChip2-pool3',
       'StanfordPedsChipRedo-pool2', 'KT151022-Chip3-2-Osprey',
       'KT151022-Chip3-3-BigBird', 'Experiment1_Pool3_8.4pM_Input'], dtype=object)
In [136]:
sorted(df_allSmpl.ix[df_allSmpl.EXPERIMENT.isin(nans_exps)].RUN_NAME.unique())
Out[136]:
['150605_M02587_0102_000000000-AE6CC',
 '150608_M02587_0103_000000000-AG0HK',
 '150619_M03241_0070_000000000-AGBAN',
 '150619_M03828_0011_000000000-AGB7D',
 '150629_M03206_0073_000000000-AGBCB',
 '150703_M03206_0075_000000000-AH332',
 '150707_M02587_0112_000000000-AH6B2',
 '150707_M03241_0075_000000000-AH2MR',
 '150709_M03241_0077_000000000-AGBAT',
 '150716_M03206_0081_000000000-AH2B9',
 '150716_M03241_0081_000000000-AH62D',
 '150721_M02587_0116_AHDT6',
 '150724_M02587_0117_000000000-AHF44',
 '150724_M03241_0083_000000000-AHCJ4',
 '150805_M02587_0119_AHGHJ',
 '150805_M03206_0085_AHJCK',
 '150805_M03241_0086_AHG81',
 '150805_M03828_0025_AHGRJ',
 '150806_M02587_0120_000000000-AHHK1',
 '150806_M02587_0120_AHHK1',
 '150806_M03206_0086_AHJV0',
 '150806_M03241_0087_AHHK0',
 '150806_M03828_0026_AHGHP',
 '150810_M02587_0121_AHGAG',
 '150810_M03206_0087_AHCCA',
 '150810_M03241_0088_AHG0D',
 '150810_M03828_0027_AHGMB',
 '150813_M02587_0122_AHUHY',
 '150813_M03206_0088_AHUC8',
 '150813_M03828_0028_AHHK3',
 '150817_M02587_0123_AHU85',
 '150817_M03241_0091_AHUNL',
 '150817_M03828_0030_AHU9E',
 '150818_M03206_0090_AHUA2',
 '150820_M03206_0091_AHJPM',
 '150820_M03241_0092_AHHJG',
 '150820_M03828_0031_AHJT1',
 '150821_M03206_0092_AHFYH',
 '150821_M03241_0093_AJ818',
 '150821_M03828_0032_AJ8KM',
 '150826_M02587_0124_AJ93R',
 '150826_M03206_0093_AJ8KB',
 '150826_M03828_0033_AJ2NT',
 '150828_M03206_0094_AHHMG',
 '150828_M03241_0094_AHJVV',
 '150828_M03828_0034_AHJRR',
 '150831_M03206_0095_AHJUY',
 '150831_M03828_0035_AHHJH',
 '150901_M03828_0036_AHJRM',
 '150903_M02587_0125_AHFNL',
 '150903_M03206_0096_AHHM6',
 '150903_M03828_0037_AHGJ5',
 '150904_M02587_0126_AJ4R0',
 '150904_M03206_0097_AJ4RN',
 '150904_M03241_0095_AJ513',
 '150909_M03206_0098_AJ524',
 '150909_M03241_0096_AJ6DL',
 '150909_M03828_0038_AJ4PH',
 '150910_M02587_0127_AJ933',
 '150910_M03206_0099_AJ3MD',
 '150910_M03241_0097_AJ96F',
 '150910_M03828_0039_AJ3PT',
 '150911_M03828_0040-AJ8JH_09-14-2015-12h50m',
 '150915_M02587_0129_AJ8LE',
 '150915_M03206_0100_AJGB3',
 '150915_M03241_0098_AJ4WN',
 '150915_M03828_0041_AJ4R8',
 '150916_M02587_0130_AGGYA',
 '150916_M03206_0101_AJ517',
 '150916_M03241_0099_AJ4WA',
 '150916_M03828_0042_AJ4RL',
 '150917_M03206_0102_AJ50Y',
 '150917_M03241_0100_AJ68Y',
 '150917_M03828_0043_AJ4W7',
 '150918_M02587_0131_AJ80U',
 '150918_M03206_0103_AJ4R4',
 '150918_M03241_0101_AJ5KG',
 '150918_M03828_0044_AJ4W3',
 '150922_M03241_0102_AJ4B0',
 '150925_M03241_0104_AJ96T',
 '150926_M03241_0105_AJ6D2',
 '150928_M03828_0049_AHHT2',
 '151002_M02587_0138_AHEGR',
 '151005_M03241_0111_AHCJD',
 '151006_M02587_0140_AHEGT',
 '151012_M03241_0117_AJVUE',
 '151102_M02587_0157_AJWBY',
 '151102_M03828_0068_AJWPC',
 '160108_M03241_0150_ALGA8']
In [7]:
t_init = timeit.default_timer()
all_SNP = pd.read_csv(seq01_SNP, sep='$')#, verbose=True)
all_SNP.info()
all_SNP.set_index('SAMPLE_NAME', inplace=True)
print_exec_time(t_init)
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 3388573 entries, 0 to 3388572
Data columns (total 36 columns):
ID                     float64
RUN_ID                 float64
EXPERIMENT_NAME        object
SAMPLE_NAME            object
AMPLICON_NAME          object
SNP_NAME               object
CHROMOSOME             object
POSITION               float64
REF                    object
ALT                    object
REF_COUNT              float64
ALT_COUNT              float64
REF_FREQ               float64
ALT_FREQ               float64
REF_ALT_READS          float64
ALL_READS              float64
ERR_COUNT              float64
ERR_FREQ_TOTAL         float64
CHROMOSOME_MOCK        object
POSITION_MOCK          float64
DONORFREQUENCY         float64
ALT_FREQ_TOTAL         float64
REF_FREQ_TOTAL         float64
DONORFREQUENCYTOTAL    float64
RECIPIENTALLELE        object
DONORALLELE            object
SUBSTITUTION           object
SNPDIRECTION           object
SAMPLE_PROJECT         float64
UNIQUEID               object
RELATIVE_COVERAGE      float64
REFALTFRACTION         float64
SNPPASSQC              bool
BACKGROUND             float64
ADJUSTEDFREQUENCY      float64
RECIPIENTGENOCALL      object
dtypes: bool(1), float64(21), object(14)
memory usage: 908.1+ MB
Execution time: 24998.14492 ms 
In [8]:
t_init = timeit.default_timer()
df_allSmpl = pd.read_csv(seq01_smpl, verbose=True, sep='$')#error_bad_lines=False)
df_allSmpl.sort_index(inplace=True, axis=1)
df_allSmpl.set_index('SAMPLE_NAME', inplace=True)
df_allSmpl = convert_result_to_float(df_allSmpl,'PCT_DD_CFDNA', div=100)
# df_allSmpl = convert_result_to_float(df_allSmpl, 'TOTAL_READS')
df_allSmpl.info(verbose=True)
print_exec_time(t_init) 
Tokenization took: 42.89 ms
Type conversion took: 100.52 ms
Parser memory cleanup took: 0.03 ms
Tokenization took: 23.84 ms
Type conversion took: 54.58 ms
Parser memory cleanup took: 0.01 ms
<class 'pandas.core.frame.DataFrame'>
Index: 16212 entries, HRZ-7-7-8ng-16054E4-400E4 to SL303-Oct-28-15
Data columns (total 103 columns):
AA_BARCODE_NAME                   object
AA_BARCODE_WELL                   object
AA_INDEX                          object
ACCEPTED_BY                       object
ACCEPTED_DATE                     object
ACCESSIONED_BY                    object
ACCESSION_NO                      object
ACCESSION_SESSION_ID              object
ACCESS_ARRAY_NUM                  float64
ANALYSIS_NUM                      object
BC_SESSION_ID                     float64
BLOOD_VOL                         float64
CFDNA_PROCESSED                   object
CFDNA_PROCESS_DATE                float64
CLUSTER_DENSITY                   float64
COLLECTION_DATE                   object
COLLECTION_TIME                   object
COMMENTS                          object
DATE_ACCESSIONED                  object
DATE_SEQUENCED                    object
DAYS_SINCE_COLLECTION             object
DD_CFDNA_PASS_QC_N_DETECT_RPT     object
DESCRIPTION                       float64
DONOR_DNA_SOURCE                  object
DONOR_RELATIONSHIP_DESCRIPTION    object
DONOR_TYPE                        object
EXPERIMENT                        object
EXP_DATE                          object
FRACDETECTABLE                    object
ID                                float64
INVESTIGATOR                      object
LAB                               object
LIBRARY_ID                        float64
LIVING_RELATED                    object
LIVING_RELATED_DESC               object
MANIFEST_BARCODE_LABEL            object
MASS_INPUT                        object
ORGAN                             object
PATIENT                           object
PATIENT_STUDY_ID                  object
PAXGENE_WEIGHT                    float64
PCT_DD_CFDNA                      float64
PCT_DD_CFDNA_PASS_QC              object
PCT_DD_CFDNA_PASS_QC_N_DETECT     object
PCT_SPIKE_DPCR                    float64
PF                                object
PLASMA_INPUT_VOL                  float64
POOL_ID                           float64
PRE_AMP_NUM                       float64
PROCESS_DATE                      object
PROJECT_NAME                      object
QC_BACKGROUND                     object
QC_BACKGROUND_VAL                 object
QC_CONTAM                         object
QC_CONTAM_NON_ZR_RECHOMO_SNPS     object
QC_DD_HIGH                        object
QC_DD_HIGH_PERCENT_RECIPHET       object
QC_LOW_INPUT                      object
QC_LOW_INPUT_2                    object
QC_LOW_INPUT_2_PCT_RECIPHET       object
QC_LOW_INPUT_COVVAR_VALUE         object
QC_RESULT                         object
QC_SUFFICIENT_SNPS                object
QC_SUFFICIENT_SNPS_RECHOMO_NUM    object
RD_SAMPLE_TYPE                    object
READS_PASS_QC                     float64
RECIPIENTHETDIVISION              object
RECIPIENT_DNA_SOURCE              object
REPORTABLE                        object
RND_PROJECT_NAME                  object
RUN_DATE                          object
RUN_ID                            object
RUN_NAME                          object
RUN_QC                            object
SAMPLENAME                        object
SAMPLE_ID                         object
SAMPLE_STATUS                     object
SAMPLE_WELL                       object
SEQUENCER                         object
SNPS_PASS_QC                      float64
SNPS_PASS_QC_PCT                  object
SNPS_RECIPHET                     object
SNPS_RECIPHET_PCT                 object
SNPS_TRIALLELIC                   object
SNPS_TRIALLELIC_PCT               object
SNPS_WITH_INSUFFICIENT_READS      object
SNPS_W_INSUFFICIENT_READS_PCT     object
STATUS                            object
STOCK_DNA_CONC                    float64
STREK_LOT_NUM                     object
STUDY_NAME                        object
TARGETED_PCT_SPIKE                float64
TEST_NAME                         object
TOTAL_READS                       float64
TTP_FILE                          object
TTP_FILE_NUM                      object
TUBE_COMMENTS                     object
TUBE_EID                          object
TUBE_EID_SEQ                      float64
TUBE_SIZE                         object
TUBE_TYPE                         object
TUBE_TYPE_NAME                    object
VISIT_ID                          float64
dtypes: float64(21), object(82)
memory usage: 12.9+ MB
Execution time: 327.34276 ms 
/Users/jcollins-macbook/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:2717: DtypeWarning:

Columns (6,7,9,16,36,38,47,51,55,61,64,66,76,79,100,102) have mixed types. Specify dtype option on import or set low_memory=False.

In [10]:
# all_SNP.corr().to_csv('all_SNP_pandas_correlation_matrix.csv')
In [10]:
df_all_AV = pd.read_clipboard()
df_all_AV.info()
<class 'pandas.core.frame.DataFrame'>
Int64Index: 180 entries, 645 to 305
Data columns (total 12 columns):
Sample_Name          180 non-null object
Sample_Name_short    180 non-null object
AA_Chip_Number       180 non-null int64
HRZ_Panel            93 non-null float64
Input_ng             93 non-null float64
dd_cfDNA             180 non-null float64
dd_cfDNA_Pass_QC     180 non-null float64
QC_Result            180 non-null object
fracDetectable       180 non-null float64
Is_Streck            180 non-null bool
mean                 1 non-null object
median               1 non-null object
dtypes: bool(1), float64(5), int64(1), object(5)
memory usage: 17.1+ KB
In [119]:
df_all = df_allSmpl[df_allSmpl.index.isin(AV_all_smpls_list)]
df_all.info()
<class 'pandas.core.frame.DataFrame'>
Index: 1927 entries, AJ61-75-92-Nov-4-15 to SL303-Oct-28-15
Columns: 103 entries, AA_BARCODE_NAME to VISIT_ID
dtypes: float64(21), object(82)
memory usage: 1.5+ MB
In [14]:
df_all_AV_blanks = df_all.copy()

Data structure cleaning

In [73]:
df_all = df_allSmpl[df_allSmpl.STUDY_NAME=='DART']
df_all.info()
<class 'pandas.core.frame.DataFrame'>
Index: 2059 entries, AH98-39-97a-2-89688 to ZE31-84-54a-2-89669
Columns: 103 entries, AA_BARCODE_NAME to VISIT_ID
dtypes: float64(21), object(82)
memory usage: 1.6+ MB
In [74]:
# df_all_KT = df_allSmpl[df_allSmpl.index.str.startswith('KT170203')]
# df_all_KT = pd.read_csv(KT_smpl, sep='\t')
# df_all_KT.info()
# df_allSmpl.QC_RESULT
In [76]:
series_all_DART = pd.read_csv(DART_lock2_smpls)
series_all_DART.info()
all_DART_list = series_all_DART.Sample_Name.values

### DART FILTER
# df_all_DART = df_allSmpl[df_allSmpl.index.str.startswith(tuple(series_all_DART.Sample_Name.values))]
df_all_DART = df_allSmpl[(df_allSmpl['TUBE_EID'].isin(all_DART_list)) 
                         & (df_allSmpl.QC_RESULT)]
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 1470 entries, 0 to 1469
Data columns (total 1 columns):
Sample_Name    1470 non-null object
dtypes: object(1)
memory usage: 11.6+ KB
In [120]:
df_bySNP = all_SNP[all_SNP.index.isin(df_all.index)]# & (all_SNP.SNPPASSQC)]
df_bySNP.info(verbose=True)
<class 'pandas.core.frame.DataFrame'>
Index: 493905 entries, HRZ-7-6-60-Oct-1-15 to NG63-03-05b-2-40184
Data columns (total 35 columns):
ID                     493905 non-null float64
RUN_ID                 493905 non-null float64
EXPERIMENT_NAME        493905 non-null object
AMPLICON_NAME          493905 non-null object
SNP_NAME               493905 non-null object
CHROMOSOME             493905 non-null object
POSITION               493905 non-null float64
REF                    493905 non-null object
ALT                    493905 non-null object
REF_COUNT              493905 non-null float64
ALT_COUNT              493905 non-null float64
REF_FREQ               493905 non-null float64
ALT_FREQ               493905 non-null float64
REF_ALT_READS          493905 non-null float64
ALL_READS              493905 non-null float64
ERR_COUNT              493905 non-null float64
ERR_FREQ_TOTAL         493905 non-null float64
CHROMOSOME_MOCK        493905 non-null object
POSITION_MOCK          493905 non-null float64
DONORFREQUENCY         493905 non-null float64
ALT_FREQ_TOTAL         493905 non-null float64
REF_FREQ_TOTAL         493905 non-null float64
DONORFREQUENCYTOTAL    493905 non-null float64
RECIPIENTALLELE        493905 non-null object
DONORALLELE            493905 non-null object
SUBSTITUTION           493905 non-null object
SNPDIRECTION           493905 non-null object
SAMPLE_PROJECT         0 non-null float64
UNIQUEID               493905 non-null object
RELATIVE_COVERAGE      493905 non-null float64
REFALTFRACTION         493905 non-null float64
SNPPASSQC              493905 non-null bool
BACKGROUND             329306 non-null float64
ADJUSTEDFREQUENCY      329306 non-null float64
RECIPIENTGENOCALL      445042 non-null object
dtypes: bool(1), float64(21), object(13)
memory usage: 132.4+ MB

distribute number of sample results

In [67]:
nans = nan_adjFreq_snps.iloc[:,0].values
nans
Out[67]:
array(['AVBlank-Aug-21-15', 'AVBlank-Aug-26-15', 'AVBlank-Aug-28-15',
       'AVBlank-Aug-31-15', 'AVBlank-Sep-15-15', 'AVBlank-Sep-16-15',
       'AVBlank-Sep-18-15', 'AVBlank-Sep-4-15', 'AVBlank-Sep-9-15',
       'AVStreck0001-Aug-20-15', 'AVStreck0001-Aug-21-15',
       'AVStreck0001-Aug-26-15', 'AVStreck0001-Aug-28-15',
       'AVStreck0001-Aug-31-15', 'AVStreck0001-Sep-18-15',
       'Streck0002-Sep-15-15', 'Streck0002-Sep-16-15',
       'Streck0002-Sep-4-15', 'Streck0002-Sep-9-15'], dtype=object)
In [15]:
# df_all.to_csv('av_blanks_sample_stats.csv')
In [38]:
df_bySNP
Out[38]:
ID RUN_ID EXPERIMENT_NAME AMPLICON_NAME SNP_NAME CHROMOSOME POSITION REF ALT REF_COUNT ALT_COUNT REF_FREQ ALT_FREQ REF_ALT_READS ALL_READS ERR_COUNT ERR_FREQ_TOTAL CHROMOSOME_MOCK POSITION_MOCK DONORFREQUENCY ALT_FREQ_TOTAL REF_FREQ_TOTAL DONORFREQUENCYTOTAL RECIPIENTALLELE DONORALLELE SUBSTITUTION SNPDIRECTION SAMPLE_PROJECT UNIQUEID RELATIVE_COVERAGE REFALTFRACTION SNPPASSQC BACKGROUND ADJUSTEDFREQUENCY RECIPIENTGENOCALL
SAMPLE_NAME
HRZ-8-1-60-Oct-1-15 2617.0 195.0 CDC30SepPool1 aIISNP102 IISNP102 chr1 154744807.0 C G 4.0 12710.0 0.000315 0.999685 12714.0 12714.0 0.0 0.000000 chr1_154744236_154745348 572.0 0.000315 0.999685 0.000315 0.000315 G C GC IISNP102 GC NaN HRZ-8-1-60-Oct-1-15 1.505214 1.000000 True 0.000165 0.000150 Recipient Homo
HRZ-8-1-60-Oct-1-15 2618.0 195.0 CDC30SepPool1 aIISNP3 IISNP3 chr1 160786670.0 A G 13694.0 2.0 0.999854 0.000146 13696.0 13697.0 1.0 0.000073 chr1_160786113_160787219 558.0 0.000146 0.000146 0.999781 0.000146 A G AG IISNP3 AG NaN HRZ-8-1-60-Oct-1-15 1.621592 0.999927 True 0.001835 -0.001689 Recipient Homo
HRZ-8-1-60-Oct-1-15 2619.0 195.0 CDC30SepPool1 aIISNP214 IISNP214 chr1 161019040.0 G C 5545.0 5243.0 0.513997 0.486003 10788.0 10790.0 2.0 0.000185 chr1_161018464_161019586 577.0 0.486003 0.485913 0.513902 0.485913 G C GC IISNP214 GC NaN HRZ-8-1-60-Oct-1-15 1.277431 0.999815 True 0.000165 0.485838 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2620.0 195.0 CDC30SepPool1 aIISNP242 IISNP242 chr1 179876988.0 C G 6129.0 5884.0 0.510197 0.489803 12013.0 12014.0 1.0 0.000083 chr1_179876419_179877532 570.0 0.489803 0.489762 0.510155 0.489762 C G CG IISNP242 CG NaN HRZ-8-1-60-Oct-1-15 1.422341 0.999917 True 0.000167 0.489636 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2621.0 195.0 CDC30SepPool1 aIISNP264 IISNP264 chr1 205554085.0 G C 4941.0 5512.0 0.472687 0.527313 10453.0 10460.0 7.0 0.000669 chr1_205553518_205554618 568.0 0.472687 0.526960 0.472371 0.472371 C G CG IISNP264 CG NaN HRZ-8-1-60-Oct-1-15 1.238362 0.999331 True 0.000167 0.472521 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2622.0 195.0 CDC30SepPool1 aIISNP257 IISNP257 chr1 214837110.0 C G 5220.0 5200.0 0.500960 0.499040 10420.0 10424.0 4.0 0.000384 chr1_214836531_214837646 580.0 0.499040 0.498849 0.500767 0.498849 C G CG IISNP257 CG NaN HRZ-8-1-60-Oct-1-15 1.234100 0.999616 True 0.000167 0.498874 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2623.0 195.0 CDC30SepPool1 aIISNP19 IISNP19 chr1 233448413.0 C T 5311.0 3129.0 0.629265 0.370735 8440.0 8443.0 3.0 0.000355 chr1_233447873_233448982 541.0 0.370735 0.370603 0.629042 0.370603 C T CT IISNP19 CT NaN HRZ-8-1-60-Oct-1-15 0.999569 0.999645 True 0.001077 0.369658 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2624.0 195.0 CDC30SepPool1 aIISNP238 IISNP238 chr1 234041422.0 G C 6089.0 6559.0 0.481420 0.518580 12648.0 12651.0 3.0 0.000237 chr1_234040863_234041981 560.0 0.481420 0.518457 0.481306 0.481306 C G CG IISNP238 CG NaN HRZ-8-1-60-Oct-1-15 1.497755 0.999763 True 0.000167 0.481253 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2625.0 195.0 CDC30SepPool1 aIISNP104 IISNP104 chr1 236381825.0 G C 2500.0 2585.0 0.491642 0.508358 5085.0 5085.0 0.0 0.000000 chr1_236381266_236382387 560.0 0.491642 0.508358 0.491642 0.491642 C G CG IISNP104 CG NaN HRZ-8-1-60-Oct-1-15 0.602015 1.000000 True 0.000167 0.491475 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2626.0 195.0 CDC30SepPool1 aIISNP83 IISNP83 chr1 239881926.0 A G 6552.0 6.0 0.999085 0.000915 6558.0 6561.0 3.0 0.000457 chr1_239881353_239882471 574.0 0.000915 0.000914 0.998628 0.000914 A G AG IISNP83 AG NaN HRZ-8-1-60-Oct-1-15 0.776759 0.999543 True 0.001835 -0.000920 Recipient Homo
HRZ-8-1-60-Oct-1-15 2627.0 195.0 CDC30SepPool1 aIISNP131 IISNP131 chr1 247752019.0 G C 4770.0 1.0 0.999790 0.000210 4771.0 4772.0 1.0 0.000210 chr1_247751483_247752601 537.0 0.000210 0.000210 0.999581 0.000210 G C GC IISNP131 GC NaN HRZ-8-1-60-Oct-1-15 0.564958 0.999790 True 0.000165 0.000045 Recipient Homo
HRZ-8-1-60-Oct-1-15 2628.0 195.0 CDC30SepPool1 aIISNP121 IISNP121 chr10 5136651.0 C G 6704.0 2.0 0.999702 0.000298 6706.0 6709.0 3.0 0.000447 chr10_5136059_5137186 593.0 0.000298 0.000298 0.999255 0.000298 C G CG IISNP121 CG NaN HRZ-8-1-60-Oct-1-15 0.794280 0.999553 True 0.000167 0.000132 Recipient Homo
HRZ-8-1-60-Oct-1-15 2629.0 195.0 CDC30SepPool1 aIISNP244 IISNP244 chr10 21414892.0 C G 10468.0 0.0 1.000000 0.000000 10468.0 10468.0 0.0 0.000000 chr10_21414322_21415442 571.0 0.000000 0.000000 1.000000 0.000000 C G CG IISNP244 CG NaN HRZ-8-1-60-Oct-1-15 1.239309 1.000000 True 0.000167 -0.000167 Recipient Homo
HRZ-8-1-60-Oct-1-15 2630.0 195.0 CDC30SepPool1 aIISNP114 IISNP114 chr10 24873369.0 C G 1881.0 1982.0 0.486927 0.513073 3863.0 3998.0 135.0 0.033767 chr10_24872787_24873906 583.0 0.486927 0.495748 0.470485 0.470485 G C GC IISNP114 GC NaN HRZ-8-1-60-Oct-1-15 0.473324 0.966233 True 0.000165 0.486763 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2631.0 195.0 CDC30SepPool1 aIISNP178 IISNP178 chr10 25701341.0 C G 0.0 4584.0 0.000000 1.000000 4584.0 4586.0 2.0 0.000436 chr10_25700758_25701869 584.0 0.000000 0.999564 0.000000 0.000000 G C GC IISNP178 GC NaN HRZ-8-1-60-Oct-1-15 0.542938 0.999564 True 0.000165 -0.000165 Recipient Homo
HRZ-8-1-60-Oct-1-15 2632.0 195.0 CDC30SepPool1 aIISNP181 IISNP181 chr10 38344700.0 C G 3414.0 3667.0 0.482135 0.517865 7081.0 7084.0 3.0 0.000423 chr10_38344113_38345242 588.0 0.482135 0.517645 0.481931 0.481931 G C GC IISNP181 GC NaN HRZ-8-1-60-Oct-1-15 0.838677 0.999577 True 0.000165 0.481971 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2633.0 195.0 CDC30SepPool1 aIISNP215 IISNP215 chr10 69934258.0 C G 4665.0 1.0 0.999786 0.000214 4666.0 4670.0 4.0 0.000857 chr10_69933675_69934782 584.0 0.000214 0.000214 0.998929 0.000214 C G CG IISNP215 CG NaN HRZ-8-1-60-Oct-1-15 0.552883 0.999143 True 0.000167 0.000048 Recipient Homo
HRZ-8-1-60-Oct-1-15 2634.0 195.0 CDC30SepPool1 aIISNP165 IISNP165 chr10 90342837.0 C G 10510.0 0.0 1.000000 0.000000 10510.0 10515.0 5.0 0.000476 chr10_90342263_90343376 575.0 0.000000 0.000000 0.999524 0.000000 C G CG IISNP165 CG NaN HRZ-8-1-60-Oct-1-15 1.244874 0.999524 True 0.000167 -0.000167 Recipient Homo
HRZ-8-1-60-Oct-1-15 2635.0 195.0 CDC30SepPool1 aIISNP35 IISNP35 chr10 97172595.0 T C 11830.0 4.0 0.999662 0.000338 11834.0 11835.0 1.0 0.000084 chr10_97172060_97173166 536.0 0.000338 0.000338 0.999578 0.000338 T C TC IISNP35 TC NaN HRZ-8-1-60-Oct-1-15 1.401149 0.999916 True 0.001818 -0.001480 Recipient Homo
HRZ-8-1-60-Oct-1-15 2636.0 195.0 CDC30SepPool1 aIISNP154 IISNP154 chr10 99439541.0 G C 13242.0 4.0 0.999698 0.000302 13246.0 13248.0 2.0 0.000151 chr10_99438974_99440086 568.0 0.000302 0.000302 0.999547 0.000302 G C GC IISNP154 GC NaN HRZ-8-1-60-Oct-1-15 1.568434 0.999849 True 0.000165 0.000137 Recipient Homo
HRZ-8-1-60-Oct-1-15 2637.0 195.0 CDC30SepPool1 aIISNP256 IISNP256 chr10 114053546.0 C G 0.0 4743.0 0.000000 1.000000 4743.0 4743.0 0.0 0.000000 chr10_114052989_114054096 558.0 0.000000 1.000000 0.000000 0.000000 G C GC IISNP256 GC NaN HRZ-8-1-60-Oct-1-15 0.561525 1.000000 True 0.000165 -0.000165 Recipient Homo
HRZ-8-1-60-Oct-1-15 2638.0 195.0 CDC30SepPool1 aIISNP189 IISNP189 chr10 126714714.0 G C 5653.0 5210.0 0.520390 0.479610 10863.0 10867.0 4.0 0.000368 chr10_126714134_126715248 581.0 0.479610 0.479433 0.520199 0.479433 G C GC IISNP189 GC NaN HRZ-8-1-60-Oct-1-15 1.286547 0.999632 True 0.000165 0.479445 Recipient Hetero
HRZ-8-1-60-Oct-1-15 2639.0 195.0 CDC30SepPool1 aIISNP204 IISNP204 chr10 128019025.0 C G 6.0 13964.0 0.000429 0.999571 13970.0 13972.0 2.0 0.000143 chr10_128018457_128019577 569.0 0.000429 0.999427 0.000429 0.000429 G C GC IISNP204 GC NaN HRZ-8-1-60-Oct-1-15 1.654149 0.999857 True 0.000165 0.000265 Recipient Homo
HRZ-8-1-8-Oct-1-15 2905.0 195.0 CDC30SepPool1 aIISNP24 IISNP24 chr11 5099393.0 T A 13536.0 4.0 0.999705 0.000295 13540.0 13544.0 4.0 0.000295 chr11_5098828_5099937 566.0 0.000295 0.000295 0.999409 0.000295 T A TA IISNP24 TA NaN HRZ-8-1-8-Oct-1-15 1.910967 0.999705 True 0.000267 0.000029 Recipient Homo
HRZ-8-1-8-Oct-1-15 2906.0 195.0 CDC30SepPool1 aIISNP38 IISNP38 chr11 5709028.0 C T 5390.0 5015.0 0.518020 0.481980 10405.0 10405.0 0.0 0.000000 chr11_5708471_5709577 558.0 0.481980 0.481980 0.518020 0.481980 C T CT IISNP38 CT NaN HRZ-8-1-8-Oct-1-15 1.468075 1.000000 True 0.001140 0.480840 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2907.0 195.0 CDC30SepPool1 aIISNP206 IISNP206 chr11 8947283.0 G C 4028.0 3817.0 0.513448 0.486552 7845.0 7847.0 2.0 0.000255 chr11_8946706_8947820 578.0 0.486552 0.486428 0.513317 0.486428 G C GC IISNP206 GC NaN HRZ-8-1-8-Oct-1-15 1.107159 0.999745 True 0.000163 0.486389 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2908.0 195.0 CDC30SepPool1 aIISNP84 IISNP84 chr11 11096221.0 C T 3913.0 4532.0 0.463351 0.536649 8445.0 8450.0 5.0 0.000592 chr11_11095660_11096769 562.0 0.463351 0.536331 0.463077 0.463077 T C TC IISNP84 TC NaN HRZ-8-1-8-Oct-1-15 1.192238 0.999408 True 0.001852 0.461499 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2909.0 195.0 CDC30SepPool1 aIISNP109 IISNP109 chr11 11292700.0 G C 11055.0 2.0 0.999819 0.000181 11057.0 11063.0 6.0 0.000542 chr11_11292148_11293259 553.0 0.000181 0.000181 0.999277 0.000181 G C GC IISNP109 GC NaN HRZ-8-1-8-Oct-1-15 1.560915 0.999458 True 0.000163 0.000018 Recipient Homo
HRZ-8-1-8-Oct-1-15 2910.0 195.0 CDC30SepPool1 aIISNP107 IISNP107 chr11 17519742.0 C G 0.0 2886.0 0.000000 1.000000 2886.0 2886.0 0.0 0.000000 chr11_17519170_17520279 573.0 0.000000 1.000000 0.000000 0.000000 G C GC IISNP107 GC NaN HRZ-8-1-8-Oct-1-15 0.407195 1.000000 True 0.000163 -0.000163 Recipient Homo
HRZ-8-1-8-Oct-1-15 2911.0 195.0 CDC30SepPool1 aIISNP127 IISNP127 chr11 57799371.0 G C 0.0 5327.0 0.000000 1.000000 5327.0 5327.0 0.0 0.000000 chr11_57798787_57799916 585.0 0.000000 1.000000 0.000000 0.000000 C G CG IISNP127 CG NaN HRZ-8-1-8-Oct-1-15 0.751604 1.000000 True 0.000151 -0.000151 Recipient Homo
HRZ-8-1-8-Oct-1-15 2912.0 195.0 CDC30SepPool1 aIISNP99 IISNP99 chr11 58318619.0 C G 4716.0 4715.0 0.500053 0.499947 9431.0 9432.0 1.0 0.000106 chr11_58318053_58319181 567.0 0.499947 0.499894 0.500000 0.499894 C G CG IISNP99 CG NaN HRZ-8-1-8-Oct-1-15 1.330792 0.999894 True 0.000151 0.499796 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2913.0 195.0 CDC30SepPool1 aIISNP236 IISNP236 chr11 65629934.0 G C 364.0 13.0 0.965517 0.034483 377.0 377.0 0.0 0.000000 chr11_65629413_65630524 522.0 0.034483 0.034483 0.965517 0.034483 G C GC IISNP236 GC NaN HRZ-8-1-8-Oct-1-15 0.053192 1.000000 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2914.0 195.0 CDC30SepPool1 aIISNP182 IISNP182 chr11 94231257.0 C G 2.0 6194.0 0.000323 0.999677 6196.0 6196.0 0.0 0.000000 chr11_94230690_94231811 568.0 0.000323 0.999677 0.000323 0.000323 G C GC IISNP182 GC NaN HRZ-8-1-8-Oct-1-15 0.874214 1.000000 True 0.000163 0.000160 Recipient Homo
HRZ-8-1-8-Oct-1-15 2915.0 195.0 CDC30SepPool1 aIISNP234 IISNP234 chr11 104869708.0 G C 8003.0 7291.0 0.523277 0.476723 15294.0 15297.0 3.0 0.000196 chr11_104869130_104870257 579.0 0.476723 0.476629 0.523174 0.476629 G C GC IISNP234 GC NaN HRZ-8-1-8-Oct-1-15 2.158303 0.999804 True 0.000163 0.476560 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2916.0 195.0 CDC30SepPool1 aIISNP73 IISNP73 chr11 105912984.0 T C 5682.0 5477.0 0.509185 0.490815 11159.0 11160.0 1.0 0.000090 chr11_105912429_105913529 556.0 0.490815 0.490771 0.509140 0.490771 T C TC IISNP73 TC NaN HRZ-8-1-8-Oct-1-15 1.574601 0.999910 True 0.001852 0.488962 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2917.0 195.0 CDC30SepPool1 aIISNP1 IISNP1 chr11 115207176.0 C G 0.0 2355.0 0.000000 1.000000 2355.0 2355.0 0.0 0.000000 chr11_115206646_115207761 531.0 0.000000 1.000000 0.000000 0.000000 G C GC IISNP1 GC NaN HRZ-8-1-8-Oct-1-15 0.332275 1.000000 True 0.000163 -0.000163 Recipient Homo
HRZ-8-1-8-Oct-1-15 2918.0 195.0 CDC30SepPool1 aIISNP245 IISNP245 chr11 117163824.0 C G 10973.0 0.0 1.000000 0.000000 10973.0 10979.0 6.0 0.000546 chr11_117163245_117164370 580.0 0.000000 0.000000 0.999454 0.000000 C G CG IISNP245 CG NaN HRZ-8-1-8-Oct-1-15 1.549063 0.999454 True 0.000151 -0.000151 Recipient Homo
HRZ-8-1-8-Oct-1-15 2919.0 195.0 CDC30SepPool1 aIISNP71 IISNP71 chr11 122195989.0 C T 1450.0 8.0 0.994513 0.005487 1458.0 1458.0 0.0 0.000000 chr11_122195414_122196543 576.0 0.005487 0.005487 0.994513 0.005487 C T CT IISNP71 CT NaN HRZ-8-1-8-Oct-1-15 0.205714 1.000000 True 0.001140 0.004347 Recipient Homo
HRZ-8-1-8-Oct-1-15 2920.0 195.0 CDC30SepPool1 aIISNP191 IISNP191 chr11 125763746.0 C G 4.0 7875.0 0.000508 0.999492 7879.0 7879.0 0.0 0.000000 chr11_125763182_125764289 565.0 0.000508 0.999492 0.000508 0.000508 G C GC IISNP191 GC NaN HRZ-8-1-8-Oct-1-15 1.111674 1.000000 True 0.000163 0.000345 Recipient Homo
HRZ-8-1-8-Oct-1-15 2921.0 195.0 CDC30SepPool1 aIISNP145 IISNP145 chr12 5021348.0 G C 0.0 6044.0 0.000000 1.000000 6044.0 6753.0 709.0 0.104990 chr12_5020815_5021938 534.0 0.000000 0.895010 0.000000 0.000000 C G CG IISNP145 CG NaN HRZ-8-1-8-Oct-1-15 0.952803 0.895010 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2922.0 195.0 CDC30SepPool1 aIISNP47 IISNP47 chr12 6909442.0 T C 6087.0 6895.0 0.468880 0.531120 12982.0 12984.0 2.0 0.000154 chr12_6908891_6910000 552.0 0.468880 0.531038 0.468808 0.468808 C T CT IISNP47 CT NaN HRZ-8-1-8-Oct-1-15 1.831955 0.999846 True 0.001140 0.467740 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2923.0 195.0 CDC30SepPool1 aIISNP48 IISNP48 chr12 6945914.0 C G 3.0 7967.0 0.000376 0.999624 7970.0 7978.0 8.0 0.001003 chr12_6945352_6946456 563.0 0.000376 0.998621 0.000376 0.000376 G C GC IISNP48 GC NaN HRZ-8-1-8-Oct-1-15 1.125642 0.998997 True 0.000163 0.000214 Recipient Homo
HRZ-8-1-8-Oct-1-15 2924.0 195.0 CDC30SepPool1 aIISNP258 IISNP258 chr12 14018777.0 G C 8020.0 0.0 1.000000 0.000000 8020.0 8026.0 6.0 0.000748 chr12_14018199_14019328 579.0 0.000000 0.000000 0.999252 0.000000 G C GC IISNP258 GC NaN HRZ-8-1-8-Oct-1-15 1.132414 0.999252 True 0.000163 -0.000163 Recipient Homo
HRZ-8-1-8-Oct-1-15 2925.0 195.0 CDC30SepPool1 aIISNP133 IISNP133 chr12 14656768.0 G C 1444.0 2.0 0.998617 0.001383 1446.0 1446.0 0.0 0.000000 chr12_14656198_14657327 571.0 0.001383 0.001383 0.998617 0.001383 G C GC IISNP133 GC NaN HRZ-8-1-8-Oct-1-15 0.204021 1.000000 True 0.000163 0.001221 Recipient Homo
HRZ-8-1-8-Oct-1-15 2926.0 195.0 CDC30SepPool1 aIISNP142 IISNP142 chr12 31249861.0 C G 2950.0 3090.0 0.488411 0.511589 6040.0 6046.0 6.0 0.000992 chr12_31249317_31250444 545.0 0.488411 0.511082 0.487926 0.487926 G C GC IISNP142 GC NaN HRZ-8-1-8-Oct-1-15 0.853050 0.999008 True 0.000163 0.488248 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2927.0 195.0 CDC30SepPool1 aIISNP132 IISNP132 chr12 49255798.0 G C 6962.0 6761.0 0.507323 0.492677 13723.0 13723.0 0.0 0.000000 chr12_49255241_49256366 558.0 0.492677 0.492677 0.507323 0.492677 G C GC IISNP132 GC NaN HRZ-8-1-8-Oct-1-15 1.936223 1.000000 True 0.000163 0.492514 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2928.0 195.0 CDC30SepPool1 aIISNP156 IISNP156 chr12 56827694.0 C G 4750.0 3481.0 0.577087 0.422913 8231.0 8231.0 0.0 0.000000 chr12_56827164_56828284 531.0 0.422913 0.422913 0.577087 0.422913 C G CG IISNP156 CG NaN HRZ-8-1-8-Oct-1-15 1.161339 1.000000 True 0.000151 0.422762 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2929.0 195.0 CDC30SepPool1 aIISNP276 IISNP276 chr12 88440676.0 G C 5088.0 5226.0 0.493310 0.506690 10314.0 10314.0 0.0 0.000000 chr12_88440104_88441233 573.0 0.493310 0.506690 0.493310 0.493310 C G CG IISNP276 CG NaN HRZ-8-1-8-Oct-1-15 1.455236 1.000000 True 0.000151 0.493159 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2930.0 195.0 CDC30SepPool1 aIISNP26 IISNP26 chr12 130761696.0 A G 5545.0 5200.0 0.516054 0.483946 10745.0 10745.0 0.0 0.000000 chr12_130761129_130762238 568.0 0.483946 0.483946 0.516054 0.483946 A G AG IISNP26 AG NaN HRZ-8-1-8-Oct-1-15 1.516047 1.000000 True 0.001817 0.482129 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2931.0 195.0 CDC30SepPool1 aIISNP125 IISNP125 chr13 25009441.0 C G 3232.0 1.0 0.999691 0.000309 3233.0 3233.0 0.0 0.000000 chr13_25008849_25009978 593.0 0.000309 0.000309 0.999691 0.000309 C G CG IISNP125 CG NaN HRZ-8-1-8-Oct-1-15 0.456154 1.000000 True 0.000151 0.000158 Recipient Homo
HRZ-8-1-8-Oct-1-15 2932.0 195.0 CDC30SepPool1 aIISNP259 IISNP259 chr13 73349359.0 G C 2237.0 0.0 1.000000 0.000000 2237.0 2238.0 1.0 0.000447 chr13_73348771_73349897 589.0 0.000000 0.000000 0.999553 0.000000 G C GC IISNP259 GC NaN HRZ-8-1-8-Oct-1-15 0.315767 0.999553 True 0.000163 -0.000163 Recipient Homo
HRZ-8-1-8-Oct-1-15 2933.0 195.0 CDC30SepPool1 aIISNP85 IISNP85 chr13 84456735.0 T C 5215.0 5924.0 0.468175 0.531825 11139.0 11139.0 0.0 0.000000 chr13_84456181_84457286 555.0 0.468175 0.531825 0.468175 0.468175 C T CT IISNP85 CT NaN HRZ-8-1-8-Oct-1-15 1.571638 1.000000 True 0.001140 0.467035 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2934.0 195.0 CDC30SepPool1 aIISNP98 IISNP98 chr14 31355096.0 C G 5116.0 3011.0 0.629507 0.370493 8127.0 8127.0 0.0 0.000000 chr14_31354504_31355624 593.0 0.370493 0.370493 0.629507 0.370493 C G CG IISNP98 CG NaN HRZ-8-1-8-Oct-1-15 1.146665 1.000000 True 0.000151 0.370342 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2935.0 195.0 CDC30SepPool1 aIISNP255 IISNP255 chr14 50799126.0 G C 3042.0 1.0 0.999671 0.000329 3043.0 3044.0 1.0 0.000329 chr14_50798535_50799661 592.0 0.000329 0.000329 0.999343 0.000329 G C GC IISNP255 GC NaN HRZ-8-1-8-Oct-1-15 0.429488 0.999671 True 0.000163 0.000166 Recipient Homo
HRZ-8-1-8-Oct-1-15 2936.0 195.0 CDC30SepPool1 aIISNP76 IISNP76 chr14 53216723.0 G C 561.0 6.0 0.989418 0.010582 567.0 567.0 0.0 0.000000 chr14_53216148_53217276 576.0 0.010582 0.010582 0.989418 0.010582 G C GC IISNP76 GC NaN HRZ-8-1-8-Oct-1-15 0.080000 1.000000 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2937.0 195.0 CDC30SepPool1 aIISNP269 IISNP269 chr14 103440473.0 G C 5884.0 2890.0 0.670618 0.329382 8774.0 8794.0 20.0 0.002274 chr14_103439920_103441032 554.0 0.329382 0.328633 0.669093 0.328633 G C GC IISNP269 GC NaN HRZ-8-1-8-Oct-1-15 1.240774 0.997726 True 0.000163 0.329220 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2938.0 195.0 CDC30SepPool1 aIISNP64 IISNP64 chr14 104769149.0 G A 4350.0 2533.0 0.631992 0.368008 6883.0 6883.0 0.0 0.000000 chr14_104768569_104769678 581.0 0.368008 0.368008 0.631992 0.368008 G A GA IISNP64 GA NaN HRZ-8-1-8-Oct-1-15 0.971145 1.000000 True 0.001125 0.366883 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2939.0 195.0 CDC30SepPool1 aIISNP161 IISNP161 chr15 22960868.0 G C 8941.0 4.0 0.999553 0.000447 8945.0 8949.0 4.0 0.000447 chr15_22960301_22961425 568.0 0.000447 0.000447 0.999106 0.000447 G C GC IISNP161 GC NaN HRZ-8-1-8-Oct-1-15 1.262643 0.999553 True 0.000163 0.000285 Recipient Homo
HRZ-8-1-8-Oct-1-15 2940.0 195.0 CDC30SepPool1 aIISNP216 IISNP216 chr15 25925094.0 C G 1866.0 3637.0 0.339088 0.660912 5503.0 5503.0 0.0 0.000000 chr15_25924513_25925623 582.0 0.339088 0.660912 0.339088 0.339088 G C GC IISNP216 GC NaN HRZ-8-1-8-Oct-1-15 0.776436 1.000000 True 0.000163 0.338925 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2941.0 195.0 CDC30SepPool1 aIISNP42 IISNP42 chr15 39313402.0 C G 12198.0 0.0 1.000000 0.000000 12198.0 12202.0 4.0 0.000328 chr15_39312848_39313954 555.0 0.000000 0.000000 0.999672 0.000000 C G CG IISNP42 CG NaN HRZ-8-1-8-Oct-1-15 1.721620 0.999672 True 0.000151 -0.000151 Recipient Homo
HRZ-8-1-8-Oct-1-15 2942.0 195.0 CDC30SepPool1 aIISNP137 IISNP137 chr15 40655873.0 G C 3955.0 0.0 1.000000 0.000000 3955.0 3959.0 4.0 0.001010 chr15_40655304_40656417 570.0 0.000000 0.000000 0.998990 0.000000 G C GC IISNP137 GC NaN HRZ-8-1-8-Oct-1-15 0.558588 0.998990 True 0.000163 -0.000163 Recipient Homo
HRZ-8-1-8-Oct-1-15 2943.0 195.0 CDC30SepPool1 aIISNP113 IISNP113 chr15 78632830.0 C G 2708.0 3234.0 0.455739 0.544261 5942.0 5942.0 0.0 0.000000 chr15_78632267_78633388 564.0 0.455739 0.544261 0.455739 0.455739 G C GC IISNP113 GC NaN HRZ-8-1-8-Oct-1-15 0.838376 1.000000 True 0.000163 0.455576 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2944.0 195.0 CDC30SepPool1 aIISNP270 IISNP270 chr15 94884108.0 G C 1.0 936.0 0.001067 0.998933 937.0 937.0 0.0 0.000000 chr15_94883526_94884639 583.0 0.001067 0.998933 0.001067 0.001067 C G CG IISNP270 CG NaN HRZ-8-1-8-Oct-1-15 0.132204 1.000000 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2945.0 195.0 CDC30SepPool1 aIISNP15 IISNP15 chr16 5868700.0 A G 6511.0 5602.0 0.537522 0.462478 12113.0 12117.0 4.0 0.000330 chr16_5868144_5869263 557.0 0.462478 0.462326 0.537344 0.462326 A G AG IISNP15 AG NaN HRZ-8-1-8-Oct-1-15 1.709627 0.999670 True 0.001817 0.460662 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2946.0 195.0 CDC30SepPool1 aIISNP75 IISNP75 chr16 7520254.0 C G 2145.0 1904.0 0.529760 0.470240 4049.0 4050.0 1.0 0.000247 chr16_7519685_7520809 570.0 0.470240 0.470123 0.529630 0.470123 C G CG IISNP75 CG NaN HRZ-8-1-8-Oct-1-15 0.571428 0.999753 True 0.000151 0.470088 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2947.0 195.0 CDC30SepPool1 aIISNP273 IISNP273 chr16 8953081.0 C G 0.0 13.0 0.000000 1.000000 13.0 13.0 0.0 0.000000 chr16_8952508_8953628 574.0 0.000000 1.000000 0.000000 0.000000 G C GC IISNP273 GC NaN HRZ-8-1-8-Oct-1-15 0.001834 1.000000 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2948.0 195.0 CDC30SepPool1 aIISNP194 IISNP194 chr16 11773662.0 C G 1434.0 1462.0 0.495166 0.504834 2896.0 2896.0 0.0 0.000000 chr16_11773071_11774198 592.0 0.495166 0.504834 0.495166 0.495166 G C GC IISNP194 GC NaN HRZ-8-1-8-Oct-1-15 0.408606 1.000000 True 0.000163 0.495003 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2949.0 195.0 CDC30SepPool1 aIISNP271 IISNP271 chr16 16278869.0 G C 1973.0 1816.0 0.520718 0.479282 3789.0 3789.0 0.0 0.000000 chr16_16278312_16279424 558.0 0.479282 0.479282 0.520718 0.479282 G C GC IISNP271 GC NaN HRZ-8-1-8-Oct-1-15 0.534602 1.000000 True 0.000163 0.479120 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2950.0 195.0 CDC30SepPool1 aIISNP12 IISNP12 chr16 78017051.0 C T 6412.0 6.0 0.999065 0.000935 6418.0 6418.0 0.0 0.000000 chr16_78016473_78017602 579.0 0.000935 0.000935 0.999065 0.000935 C T CT IISNP12 CT NaN HRZ-8-1-8-Oct-1-15 0.905536 1.000000 True 0.001140 -0.000205 Recipient Homo
HRZ-8-1-8-Oct-1-15 2951.0 195.0 CDC30SepPool1 aIISNP224 IISNP224 chr16 84522897.0 G C 2931.0 3828.0 0.433644 0.566356 6759.0 6759.0 0.0 0.000000 chr16_84522346_84523470 552.0 0.433644 0.566356 0.433644 0.433644 C G CG IISNP224 CG NaN HRZ-8-1-8-Oct-1-15 0.953649 1.000000 True 0.000151 0.433493 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2952.0 195.0 CDC30SepPool1 aIISNP168 IISNP168 chr16 88767769.0 G C 3507.0 4.0 0.998861 0.001139 3511.0 3515.0 4.0 0.001138 chr16_88767192_88768321 578.0 0.001139 0.001138 0.997724 0.001138 G C GC IISNP168 GC NaN HRZ-8-1-8-Oct-1-15 0.495943 0.998862 True 0.000163 0.000977 Recipient Homo
HRZ-8-1-8-Oct-1-15 2953.0 195.0 CDC30SepPool1 aIISNP90 IISNP90 chr17 2919393.0 A G 3595.0 6693.0 0.349436 0.650564 10288.0 10288.0 0.0 0.000000 chr17_2918812_2919921 582.0 0.349436 0.650564 0.349436 0.349436 G A GA IISNP90 GA NaN HRZ-8-1-8-Oct-1-15 1.451567 1.000000 True 0.001125 0.348311 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2954.0 195.0 CDC30SepPool1 aIISNP67 IISNP67 chr17 6811529.0 G A 149.0 25.0 0.856322 0.143678 174.0 174.0 0.0 0.000000 chr17_6810940_6812066 590.0 0.143678 0.143678 0.856322 0.143678 G A GA IISNP67 GA NaN HRZ-8-1-8-Oct-1-15 0.024550 1.000000 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2955.0 195.0 CDC30SepPool1 aIISNP210 IISNP210 chr17 7460517.0 G C 532.0 498.0 0.516505 0.483495 1030.0 1030.0 0.0 0.000000 chr17_7459983_7461095 535.0 0.483495 0.483495 0.516505 0.483495 G C GC IISNP210 GC NaN HRZ-8-1-8-Oct-1-15 0.145326 1.000000 True 0.000163 0.483333 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2956.0 195.0 CDC30SepPool1 aIISNP170 IISNP170 chr17 15217437.0 C G 10250.0 14.0 0.998636 0.001364 10264.0 10274.0 10.0 0.000973 chr17_15216858_15217965 580.0 0.001364 0.001363 0.997664 0.001363 C G CG IISNP170 CG NaN HRZ-8-1-8-Oct-1-15 1.449592 0.999027 True 0.000151 0.001213 Recipient Homo
HRZ-8-1-8-Oct-1-15 2957.0 195.0 CDC30SepPool1 aIISNP209 IISNP209 chr17 17696531.0 G C 999.0 1307.0 0.433218 0.566782 2306.0 2308.0 2.0 0.000867 chr17_17695991_17697117 541.0 0.433218 0.566291 0.432842 0.432842 C G CG IISNP209 CG NaN HRZ-8-1-8-Oct-1-15 0.325643 0.999133 True 0.000151 0.433066 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2958.0 195.0 CDC30SepPool1 aIISNP101 IISNP101 chr17 33998802.0 G C 15990.0 1.0 0.999937 0.000063 15991.0 16008.0 17.0 0.001062 chr17_33998221_33999330 582.0 0.000063 0.000062 0.998876 0.000062 G C GC IISNP101 GC NaN HRZ-8-1-8-Oct-1-15 2.258621 0.998938 True 0.000163 -0.000100 Recipient Homo
HRZ-8-1-8-Oct-1-15 2959.0 195.0 CDC30SepPool1 aIISNP192 IISNP192 chr17 35902225.0 C G 3267.0 9.0 0.997253 0.002747 3276.0 3279.0 3.0 0.000915 chr17_35901690_35902813 536.0 0.002747 0.002745 0.996340 0.002745 C G CG IISNP192 CG NaN HRZ-8-1-8-Oct-1-15 0.462645 0.999085 True 0.000151 0.002596 Recipient Homo
HRZ-8-1-8-Oct-1-15 2960.0 195.0 CDC30SepPool1 aIISNP46 IISNP46 chr17 41286822.0 T G 5630.0 447.0 0.926444 0.073556 6077.0 6082.0 5.0 0.000822 chr17_41286243_41287360 580.0 0.073556 0.073496 0.925682 0.073496 T G TG IISNP46 TG NaN HRZ-8-1-8-Oct-1-15 0.858129 0.999178 True 0.000146 0.073410 Recipient Homo
HRZ-8-1-8-Oct-1-15 2961.0 195.0 CDC30SepPool1 aIISNP81 IISNP81 chr17 41341984.0 A G 7427.0 4.0 0.999462 0.000538 7431.0 7432.0 1.0 0.000135 chr17_41341424_41342523 561.0 0.000538 0.000538 0.999327 0.000538 A G AG IISNP81 AG NaN HRZ-8-1-8-Oct-1-15 1.048605 0.999865 True 0.001817 -0.001278 Recipient Homo
HRZ-8-1-8-Oct-1-15 2962.0 195.0 CDC30SepPool1 aIISNP21 IISNP21 chr17 41691526.0 G A 6.0 9664.0 0.000620 0.999380 9670.0 9670.0 0.0 0.000000 chr17_41690968_41692073 559.0 0.000620 0.999380 0.000620 0.000620 A G AG IISNP21 AG NaN HRZ-8-1-8-Oct-1-15 1.364372 1.000000 True 0.001817 -0.001196 Recipient Homo
HRZ-8-1-8-Oct-1-15 2963.0 195.0 CDC30SepPool1 aIISNP278 IISNP278 chr17 42475983.0 G C 5066.0 5436.0 0.482384 0.517616 10502.0 10504.0 2.0 0.000190 chr17_42475406_42476535 578.0 0.482384 0.517517 0.482292 0.482292 C G CG IISNP278 CG NaN HRZ-8-1-8-Oct-1-15 1.482043 0.999810 True 0.000151 0.482233 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2964.0 195.0 CDC30SepPool1 aIISNP23 IISNP23 chr17 46510697.0 A G 6977.0 7500.0 0.481937 0.518063 14477.0 14482.0 5.0 0.000345 chr17_46510138_46511265 560.0 0.481937 0.517884 0.481770 0.481770 G A GA IISNP23 GA NaN HRZ-8-1-8-Oct-1-15 2.043312 0.999655 True 0.001125 0.480812 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2965.0 195.0 CDC30SepPool1 aIISNP272 IISNP272 chr17 48625928.0 C G 537.0 732.0 0.423168 0.576832 1269.0 1269.0 0.0 0.000000 chr17_48625341_48626470 588.0 0.423168 0.576832 0.423168 0.423168 G C GC IISNP272 GC NaN HRZ-8-1-8-Oct-1-15 0.179047 1.000000 True 0.000163 0.423005 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2966.0 195.0 CDC30SepPool1 aIISNP262 IISNP262 chr17 71232881.0 G C 2.0 10703.0 0.000187 0.999813 10705.0 10707.0 2.0 0.000187 chr17_71232306_71233435 576.0 0.000187 0.999626 0.000187 0.000187 C G CG IISNP262 CG NaN HRZ-8-1-8-Oct-1-15 1.510685 0.999813 True 0.000151 0.000035 Recipient Homo
HRZ-8-1-8-Oct-1-15 2967.0 195.0 CDC30SepPool1 aIISNP160 IISNP160 chr17 76449505.0 G C 5524.0 4883.0 0.530797 0.469203 10407.0 10408.0 1.0 0.000096 chr17_76448943_76450062 563.0 0.469203 0.469158 0.530746 0.469158 G C GC IISNP160 GC NaN HRZ-8-1-8-Oct-1-15 1.468499 0.999904 True 0.000163 0.469041 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2968.0 195.0 CDC30SepPool1 aIISNP230 IISNP230 chr17 78319380.0 G C 5153.0 5956.0 0.463858 0.536142 11109.0 11113.0 4.0 0.000360 chr17_78318816_78319925 565.0 0.463858 0.535949 0.463691 0.463691 C G CG IISNP230 CG NaN HRZ-8-1-8-Oct-1-15 1.567969 0.999640 True 0.000151 0.463707 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2969.0 195.0 CDC30SepPool1 aIISNP82 IISNP82 chr17 80461935.0 C T 1301.0 1505.0 0.463649 0.536351 2806.0 2807.0 1.0 0.000356 chr17_80461344_80462465 592.0 0.463649 0.536160 0.463484 0.463484 T C TC IISNP82 TC NaN HRZ-8-1-8-Oct-1-15 0.396049 0.999644 True 0.001852 0.461797 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2970.0 195.0 CDC30SepPool1 aIISNP51 IISNP51 chr17 80526139.0 A G 1362.0 1274.0 0.516692 0.483308 2636.0 2636.0 0.0 0.000000 chr17_80525564_80526669 576.0 0.483308 0.483308 0.516692 0.483308 A G AG IISNP51 AG NaN HRZ-8-1-8-Oct-1-15 0.371922 1.000000 True 0.001817 0.481491 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2971.0 195.0 CDC30SepPool1 aIISNP66 IISNP66 chr17 80531643.0 C G 1798.0 1661.0 0.519803 0.480197 3459.0 3459.0 0.0 0.000000 chr17_80531082_80532207 562.0 0.480197 0.480197 0.519803 0.480197 C G CG IISNP66 CG NaN HRZ-8-1-8-Oct-1-15 0.488042 1.000000 True 0.000151 0.480045 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2972.0 195.0 CDC30SepPool1 aIISNP74 IISNP74 chr17 80715702.0 G C 8757.0 0.0 1.000000 0.000000 8757.0 8763.0 6.0 0.000685 chr17_80715140_80716246 563.0 0.000000 0.000000 0.999315 0.000000 G C GC IISNP74 GC NaN HRZ-8-1-8-Oct-1-15 1.236400 0.999315 True 0.000163 -0.000163 Recipient Homo
HRZ-8-1-8-Oct-1-15 2973.0 195.0 CDC30SepPool1 aIISNP52 IISNP52 chr17 80765788.0 T C 9556.0 7.0 0.999268 0.000732 9563.0 9563.0 0.0 0.000000 chr17_80765219_80766321 570.0 0.000732 0.000732 0.999268 0.000732 T C TC IISNP52 TC NaN HRZ-8-1-8-Oct-1-15 1.349275 1.000000 True 0.001852 -0.001120 Recipient Homo
HRZ-8-1-8-Oct-1-15 2974.0 195.0 CDC30SepPool1 aIISNP92 IISNP92 chr18 9749879.0 G A 6318.0 6627.0 0.488065 0.511935 12945.0 12948.0 3.0 0.000232 chr18_9749309_9750416 571.0 0.488065 0.511816 0.487952 0.487952 A G AG IISNP92 AG NaN HRZ-8-1-8-Oct-1-15 1.826875 0.999768 True 0.001817 0.486248 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2975.0 195.0 CDC30SepPool1 aIISNP87 IISNP87 chr18 29311034.0 G A 8.0 8146.0 0.000981 0.999019 8154.0 8157.0 3.0 0.000368 chr18_29310484_29311587 551.0 0.000981 0.998651 0.000981 0.000981 A G AG IISNP87 AG NaN HRZ-8-1-8-Oct-1-15 1.150898 0.999632 True 0.001817 -0.000836 Recipient Homo
HRZ-8-1-8-Oct-1-15 2976.0 195.0 CDC30SepPool1 aIISNP186 IISNP186 chr18 44561100.0 C G 6829.0 49.0 0.992876 0.007124 6878.0 6882.0 4.0 0.000581 chr18_44560549_44561667 552.0 0.007124 0.007120 0.992299 0.007120 C G CG IISNP186 CG NaN HRZ-8-1-8-Oct-1-15 0.971004 0.999419 True 0.000151 0.006973 Recipient Homo
HRZ-8-1-8-Oct-1-15 2977.0 195.0 CDC30SepPool1 aIISNP69 IISNP69 chr18 47371014.0 C G 1.0 7615.0 0.000131 0.999869 7616.0 7620.0 4.0 0.000525 chr18_47370442_47371541 573.0 0.000131 0.999344 0.000131 0.000131 G C GC IISNP69 GC NaN HRZ-8-1-8-Oct-1-15 1.075131 0.999475 True 0.000163 -0.000031 Recipient Homo
HRZ-8-1-8-Oct-1-15 2978.0 195.0 CDC30SepPool1 aIISNP232 IISNP232 chr18 48333203.0 C G 6686.0 1.0 0.999850 0.000150 6687.0 6787.0 100.0 0.014734 chr18_48332670_48333785 534.0 0.000150 0.000147 0.985119 0.000147 C G CG IISNP232 CG NaN HRZ-8-1-8-Oct-1-15 0.957600 0.985266 True 0.000151 -0.000002 Recipient Homo
HRZ-8-1-8-Oct-1-15 2979.0 195.0 CDC30SepPool1 aIISNP41 IISNP41 chr18 55225777.0 T C 12564.0 51.0 0.995957 0.004043 12615.0 12615.0 0.0 0.000000 chr18_55225209_55226308 569.0 0.004043 0.004043 0.995957 0.004043 T C TC IISNP41 TC NaN HRZ-8-1-8-Oct-1-15 1.779891 1.000000 True 0.001852 0.002190 Recipient Homo
HRZ-8-1-8-Oct-1-15 2980.0 195.0 CDC30SepPool1 aIISNP211 IISNP211 chr18 56204945.0 C G 0.0 10304.0 0.000000 1.000000 10304.0 10304.0 0.0 0.000000 chr18_56204367_56205474 579.0 0.000000 1.000000 0.000000 0.000000 G C GC IISNP211 GC NaN HRZ-8-1-8-Oct-1-15 1.453825 1.000000 True 0.000163 -0.000163 Recipient Homo
HRZ-8-1-8-Oct-1-15 2981.0 195.0 CDC30SepPool1 aIISNP130 IISNP130 chr19 619021.0 G C 218.0 256.0 0.459916 0.540084 474.0 474.0 0.0 0.000000 chr19_618466_619585 556.0 0.459916 0.540084 0.459916 0.459916 C G CG IISNP130 CG NaN HRZ-8-1-8-Oct-1-15 0.066878 1.000000 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2982.0 195.0 CDC30SepPool1 aIISNP226 IISNP226 chr19 7986638.0 C G 226.0 0.0 1.000000 0.000000 226.0 226.0 0.0 0.000000 chr19_7986080_7987202 559.0 0.000000 0.000000 1.000000 0.000000 C G CG IISNP226 CG NaN HRZ-8-1-8-Oct-1-15 0.031887 1.000000 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2983.0 195.0 CDC30SepPool1 aIISNP159 IISNP159 chr19 10084292.0 C G 15087.0 6.0 0.999602 0.000398 15093.0 15107.0 14.0 0.000927 chr19_10083723_10084832 570.0 0.000398 0.000397 0.998676 0.000397 C G CG IISNP159 CG NaN HRZ-8-1-8-Oct-1-15 2.131496 0.999073 True 0.000151 0.000246 Recipient Homo
HRZ-8-1-8-Oct-1-15 2984.0 195.0 CDC30SepPool1 aIISNP100 IISNP100 chr19 10600442.0 G C 5447.0 0.0 1.000000 0.000000 5447.0 5447.0 0.0 0.000000 chr19_10599851_10600965 592.0 0.000000 0.000000 1.000000 0.000000 G C GC IISNP100 GC NaN HRZ-8-1-8-Oct-1-15 0.768535 1.000000 True 0.000163 -0.000163 Recipient Homo
HRZ-8-1-8-Oct-1-15 2985.0 195.0 CDC30SepPool1 aIISNP217 IISNP217 chr19 10670184.0 C G 271.0 0.0 1.000000 0.000000 271.0 271.0 0.0 0.000000 chr19_10669614_10670743 571.0 0.000000 0.000000 1.000000 0.000000 C G CG IISNP217 CG NaN HRZ-8-1-8-Oct-1-15 0.038236 1.000000 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2986.0 195.0 CDC30SepPool1 aIISNP274 IISNP274 chr19 18377647.0 G C 2.0 2904.0 0.000688 0.999312 2906.0 2913.0 7.0 0.002403 chr19_18377056_18378185 592.0 0.000688 0.996910 0.000687 0.000687 C G CG IISNP274 CG NaN HRZ-8-1-8-Oct-1-15 0.411005 0.997597 True 0.000151 0.000537 Recipient Homo
HRZ-8-1-8-Oct-1-15 2987.0 195.0 CDC30SepPool1 aIISNP171 IISNP171 chr19 36278470.0 C G 143.0 407.0 0.260000 0.740000 550.0 552.0 2.0 0.003623 chr19_36277889_36279010 582.0 0.260000 0.737319 0.259058 0.259058 G C GC IISNP171 GC NaN HRZ-8-1-8-Oct-1-15 0.077883 0.996377 False NaN NaN NaN
HRZ-8-1-8-Oct-1-15 2988.0 195.0 CDC30SepPool1 aIISNP13 IISNP13 chr19 39559807.0 A C 6010.0 5077.0 0.542076 0.457924 11087.0 11103.0 16.0 0.001441 chr19_39559236_39560337 572.0 0.457924 0.457264 0.541295 0.457264 A C AC IISNP13 AC NaN HRZ-8-1-8-Oct-1-15 1.566558 0.998559 True 0.000148 0.457776 Recipient Hetero
HRZ-8-1-8-Oct-1-15 2989.0 195.0 CDC30SepPool1 aIISNP95 IISNP95 chr19 41939297.0 C G 5.0 5074.0 0.000984 0.999016 5079.0 5082.0 3.0 0.000590 chr19_41938759_41939869 539.0 0.000984 0.998426 0.000984 0.000984 G C GC IISNP95 GC NaN HRZ-8-1-8-Oct-1-15 0.717036 0.999410 True 0.000163 0.000822 Recipient Homo
HRZ-8-1-8-Oct-1-15 2990.0 195.0 CDC30SepPool1 aIISNP117 IISNP117 chr19 44303066.0 C G 902.0 1853.0 0.327405 0.672595 2755.0 2756.0 1.0 0.000363 chr19_44302506_44303626 561.0 0.327405 0.672351 0.327286 0.327286 G C GC IISNP117 GC NaN HRZ-8-1-8-Oct-1-15 0.388853 0.999637 True 0.000163 0.327242 Recipient Hetero
Streck-4-Oct-1-15 4127.0 195.0 CDC30SepPool1 aIISNP202 IISNP202 chr6 76660551.0 G C 4394.0 4716.0 0.482327 0.517673 9110.0 9110.0 0.0 0.000000 chr6_76659989_76661118 563.0 0.482327 0.517673 0.482327 0.482327 C G CG IISNP202 CG NaN Streck-4-Oct-1-15 1.121965 1.000000 True 0.000147 0.482180 Recipient Hetero
Streck-4-Oct-1-15 4128.0 195.0 CDC30SepPool1 aIISNP36 IISNP36 chr6 120560694.0 T A 7955.0 15.0 0.998118 0.001882 7970.0 7972.0 2.0 0.000251 chr6_120560128_120561231 567.0 0.001882 0.001882 0.997868 0.001882 T A TA IISNP36 TA NaN Streck-4-Oct-1-15 0.981812 0.999749 True 0.000300 0.001583 Recipient Homo
Streck-4-Oct-1-15 4129.0 195.0 CDC30SepPool1 aIISNP34 IISNP34 chr6 123894978.0 C A 1768.0 5.0 0.997180 0.002820 1773.0 1773.0 0.0 0.000000 chr6_123894407_123895512 572.0 0.002820 0.002820 0.997180 0.002820 C A CA IISNP34 CA NaN Streck-4-Oct-1-15 0.218358 1.000000 True 0.000338 0.002482 Recipient Homo
Streck-4-Oct-1-15 4130.0 195.0 CDC30SepPool1 aIISNP164 IISNP164 chr6 126278230.0 G C 3369.0 3014.0 0.527808 0.472192 6383.0 6384.0 1.0 0.000157 chr6_126277677_126278784 554.0 0.472192 0.472118 0.527726 0.472118 G C GC IISNP164 GC NaN Streck-4-Oct-1-15 0.786237 0.999843 True 0.000167 0.472025 Recipient Hetero
Streck-4-Oct-1-15 4131.0 195.0 CDC30SepPool1 aIISNP54 IISNP54 chr6 127463376.0 C A 1087.0 432.0 0.715602 0.284398 1519.0 1519.0 0.0 0.000000 chr6_127462805_127463913 572.0 0.284398 0.284398 0.715602 0.284398 C A CA IISNP54 CA NaN Streck-4-Oct-1-15 0.187076 1.000000 True 0.000338 0.284060 Recipient Hetero
Streck-4-Oct-1-15 4132.0 195.0 CDC30SepPool1 aIISNP247 IISNP247 chr6 138413333.0 G C 10523.0 13086.0 0.445720 0.554280 23609.0 23646.0 37.0 0.001565 chr6_138412785_138413907 549.0 0.445720 0.553413 0.445022 0.445022 C G CG IISNP247 CG NaN Streck-4-Oct-1-15 2.912182 0.998435 True 0.000147 0.445573 Recipient Hetero
Streck-4-Oct-1-15 4133.0 195.0 CDC30SepPool1 aIISNP50 IISNP50 chr6 148761456.0 G C 5321.0 4351.0 0.550145 0.449855 9672.0 9684.0 12.0 0.001239 chr6_148760890_148761999 567.0 0.449855 0.449298 0.549463 0.449298 G C GC IISNP50 GC NaN Streck-4-Oct-1-15 1.192657 0.998761 True 0.000167 0.449688 Recipient Hetero
Streck-4-Oct-1-15 4134.0 195.0 CDC30SepPool1 aIISNP172 IISNP172 chr6 150209717.0 C G 1400.0 1277.0 0.522973 0.477027 2677.0 2677.0 0.0 0.000000 chr6_150209159_150210278 559.0 0.477027 0.477027 0.522973 0.477027 C G CG IISNP172 CG NaN Streck-4-Oct-1-15 0.329693 1.000000 True 0.000147 0.476880 Recipient Hetero
Streck-4-Oct-1-15 4135.0 195.0 CDC30SepPool1 aIISNP45 IISNP45 chr6 152697706.0 C T 9539.0 15.0 0.998430 0.001570 9554.0 9558.0 4.0 0.000418 chr6_152697130_152698240 577.0 0.001570 0.001569 0.998012 0.001569 C T CT IISNP45 CT NaN Streck-4-Oct-1-15 1.177139 0.999582 True 0.001080 0.000490 Recipient Homo
Streck-4-Oct-1-15 4136.0 195.0 CDC30SepPool1 aIISNP122 IISNP122 chr6 170862300.0 G C 7379.0 4601.0 0.615943 0.384057 11980.0 11986.0 6.0 0.000501 chr6_170861722_170862832 579.0 0.384057 0.383865 0.615635 0.383865 G C GC IISNP122 GC NaN Streck-4-Oct-1-15 1.476166 0.999499 True 0.000167 0.383890 Recipient Hetero
Streck-4-Oct-1-15 4137.0 195.0 CDC30SepPool1 aIISNP267 IISNP267 chr7 4026944.0 C G 4255.0 4762.0 0.471886 0.528114 9017.0 9030.0 13.0 0.001440 chr7_4026399_4027521 546.0 0.471886 0.527353 0.471207 0.471207 G C GC IISNP267 GC NaN Streck-4-Oct-1-15 1.112112 0.998560 True 0.000167 0.471719 Recipient Hetero
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
AVBlank2-Nov-10-15 725.0 288.0 CYC10Nov2015Pool3 aIISNP176 IISNP176 chr5 75932965.0 G C 9057.0 7745.0 0.539043 0.460957 16802.0 16806.0 4.0 0.000238 chr5_75932415_75933522 551.0 0.460957 0.460847 0.538915 0.460847 G C GC IISNP176 GC NaN AVBlank2-Nov-10-15 2.069358 0.999762 True 0.000182 0.460775 Recipient Hetero
AVBlank2-Nov-10-15 726.0 288.0 CYC10Nov2015Pool3 aIISNP179 IISNP179 chr5 78340257.0 C G 9736.0 18.0 0.998155 0.001845 9754.0 9765.0 11.0 0.001126 chr5_78339702_78340831 556.0 0.001845 0.001843 0.997030 0.001843 C G CG IISNP179 CG NaN AVBlank2-Nov-10-15 1.202385 0.998874 True 0.000187 0.001658 Recipient Homo
AVBlank2-Nov-10-15 727.0 288.0 CYC10Nov2015Pool3 aIISNP9 IISNP9 chr5 136633338.0 G A 5317.0 5170.0 0.507009 0.492991 10487.0 10489.0 2.0 0.000191 chr5_136632784_136633892 555.0 0.492991 0.492897 0.506912 0.492897 G A GA IISNP9 GA NaN AVBlank2-Nov-10-15 1.291532 0.999809 True 0.000987 0.492004 Recipient Hetero
AVBlank2-Nov-10-15 728.0 288.0 CYC10Nov2015Pool3 aIISNP177 IISNP177 chr5 140531746.0 C G 762.0 408.0 0.651282 0.348718 1170.0 1171.0 1.0 0.000854 chr5_140531170_140532269 577.0 0.348718 0.348420 0.650726 0.348420 C G CG IISNP177 CG NaN AVBlank2-Nov-10-15 0.144188 0.999146 True 0.000187 0.348531 Recipient Hetero
AVBlank2-Nov-10-15 729.0 288.0 CYC10Nov2015Pool3 aIISNP106 IISNP106 chr5 145442203.0 G C 9.0 9476.0 0.000949 0.999051 9485.0 9493.0 8.0 0.000843 chr5_145441622_145442735 582.0 0.000949 0.998209 0.000948 0.000948 C G CG IISNP106 CG NaN AVBlank2-Nov-10-15 1.168893 0.999157 True 0.000187 0.000762 Recipient Homo
AVBlank2-Nov-10-15 730.0 288.0 CYC10Nov2015Pool3 aIISNP80 IISNP80 chr5 159487953.0 G A 2.0 863.0 0.002312 0.997688 865.0 865.0 0.0 0.000000 chr5_159487382_159488507 572.0 0.002312 0.997688 0.002312 0.002312 A G AG IISNP80 AG NaN AVBlank2-Nov-10-15 0.106509 1.000000 False NaN NaN NaN
AVBlank2-Nov-10-15 731.0 288.0 CYC10Nov2015Pool3 aIISNP123 IISNP123 chr5 161119125.0 C G 2007.0 2129.0 0.485251 0.514749 4136.0 4136.0 0.0 0.000000 chr5_161118544_161119671 582.0 0.485251 0.514749 0.485251 0.485251 G C GC IISNP123 GC NaN AVBlank2-Nov-10-15 0.509274 1.000000 True 0.000182 0.485069 Recipient Hetero
AVBlank2-Nov-10-15 732.0 288.0 CYC10Nov2015Pool3 aIISNP58 IISNP58 chr5 169735920.0 A C 6758.0 6390.0 0.513995 0.486005 13148.0 13150.0 2.0 0.000152 chr5_169735367_169736476 554.0 0.486005 0.485932 0.513916 0.485932 A C AC IISNP58 AC NaN AVBlank2-Nov-10-15 1.619187 0.999848 True 0.000181 0.485824 Recipient Hetero
AVBlank2-Nov-10-15 733.0 288.0 CYC10Nov2015Pool3 aIISNP115 IISNP115 chr5 176863519.0 G C 2.0 5661.0 0.000353 0.999647 5663.0 5668.0 5.0 0.000882 chr5_176862952_176864062 568.0 0.000353 0.998765 0.000353 0.000353 C G CG IISNP115 CG NaN AVBlank2-Nov-10-15 0.697913 0.999118 True 0.000187 0.000166 Recipient Homo
AVBlank2-Nov-10-15 525.0 288.0 CYC10Nov2015Pool3 aIISNP79 IISNP79 chr1 14155402.0 G A 17.0 10112.0 0.001678 0.998322 10129.0 10129.0 0.0 0.000000 chr1_14154833_14155962 570.0 0.001678 0.998322 0.001678 0.001678 A G AG IISNP79 AG NaN AVBlank2-Nov-10-15 1.247205 1.000000 True 0.001456 0.000222 Recipient Homo
AVBlank2-Nov-10-15 526.0 288.0 CYC10Nov2015Pool3 aIISNP275 IISNP275 chr1 17660499.0 G C 10608.0 11371.0 0.482643 0.517357 21979.0 22014.0 35.0 0.001590 chr1_17659939_17661046 561.0 0.482643 0.516535 0.481875 0.481875 C G CG IISNP275 CG NaN AVBlank2-Nov-10-15 2.710629 0.998410 True 0.000187 0.482456 Recipient Hetero
AVBlank2-Nov-10-15 527.0 288.0 CYC10Nov2015Pool3 aIISNP96 IISNP96 chr1 19447843.0 C G 8804.0 8854.0 0.498584 0.501416 17658.0 17663.0 5.0 0.000283 chr1_19447280_19448406 564.0 0.498584 0.501274 0.498443 0.498443 G C GC IISNP96 GC NaN AVBlank2-Nov-10-15 2.174882 0.999717 True 0.000182 0.498402 Recipient Hetero
AVBlank2-Nov-10-15 528.0 288.0 CYC10Nov2015Pool3 aIISNP152 IISNP152 chr1 22216604.0 C G 2.0 2353.0 0.000849 0.999151 2355.0 2355.0 0.0 0.000000 chr1_22216012_22217133 593.0 0.000849 0.999151 0.000849 0.000849 G C GC IISNP152 GC NaN AVBlank2-Nov-10-15 0.289976 1.000000 True 0.000182 0.000667 Recipient Homo
AVBlank2-Nov-10-15 529.0 288.0 CYC10Nov2015Pool3 aIISNP265 IISNP265 chr1 47799639.0 G C 1062.0 1049.0 0.503079 0.496921 2111.0 2113.0 2.0 0.000947 chr1_47799106_47800221 534.0 0.496921 0.496451 0.502603 0.496451 G C GC IISNP265 GC NaN AVBlank2-Nov-10-15 0.260178 0.999053 True 0.000182 0.496739 Recipient Hetero
AVBlank2-Nov-10-15 530.0 288.0 CYC10Nov2015Pool3 aIISNP180 IISNP180 chr1 62516683.0 G C 18667.0 6.0 0.999679 0.000321 18673.0 18673.0 0.0 0.000000 chr1_62516111_62517226 573.0 0.000321 0.000321 0.999679 0.000321 G C GC IISNP180 GC NaN AVBlank2-Nov-10-15 2.299245 1.000000 True 0.000182 0.000139 Recipient Homo
AVBlank2-Nov-10-15 531.0 288.0 CYC10Nov2015Pool3 aIISNP111 IISNP111 chr1 75097426.0 G C 11844.0 44.0 0.996299 0.003701 11888.0 11924.0 36.0 0.003019 chr1_75096893_75098000 534.0 0.003701 0.003690 0.993291 0.003690 G C GC IISNP111 GC NaN AVBlank2-Nov-10-15 1.468227 0.996981 True 0.000182 0.003519 Recipient Homo
AVBlank2-Nov-10-15 532.0 288.0 CYC10Nov2015Pool3 aIISNP162 IISNP162 chr1 87101375.0 C G 11.0 23125.0 0.000475 0.999525 23136.0 23139.0 3.0 0.000130 chr1_87100813_87101939 563.0 0.000475 0.999395 0.000475 0.000475 G C GC IISNP162 GC NaN AVBlank2-Nov-10-15 2.849153 0.999870 True 0.000182 0.000293 Recipient Homo
AVBlank2-Nov-10-15 533.0 288.0 CYC10Nov2015Pool3 aIISNP68 IISNP68 chr1 105717631.0 A G 1616.0 3366.0 0.324368 0.675632 4982.0 4984.0 2.0 0.000401 chr1_105717077_105718184 555.0 0.324368 0.675361 0.324238 0.324238 G A GA IISNP68 GA NaN AVBlank2-Nov-10-15 0.613690 0.999599 True 0.000987 0.323380 Recipient Hetero
AVBlank2-Nov-10-15 534.0 288.0 CYC10Nov2015Pool3 aIISNP268 IISNP268 chr1 111957097.0 C G 10663.0 9200.0 0.536827 0.463173 19863.0 19870.0 7.0 0.000352 chr1_111956532_111957661 566.0 0.463173 0.463010 0.536638 0.463010 C G CG IISNP268 CG NaN AVBlank2-Nov-10-15 2.446634 0.999648 True 0.000187 0.462986 Recipient Hetero
AVBlank2-Nov-10-15 535.0 288.0 CYC10Nov2015Pool3 aIISNP222 IISNP222 chr1 150526044.0 G C 6372.0 5156.0 0.552741 0.447259 11528.0 11537.0 9.0 0.000780 chr1_150525491_150526617 554.0 0.447259 0.446910 0.552310 0.446910 G C GC IISNP222 GC NaN AVBlank2-Nov-10-15 1.420575 0.999220 True 0.000182 0.447077 Recipient Hetero
AVBlank2-Nov-10-15 536.0 288.0 CYC10Nov2015Pool3 aIISNP227 IISNP227 chr1 152732436.0 G C 4069.0 4023.0 0.502842 0.497158 8092.0 8097.0 5.0 0.000618 chr1_152731903_152733020 534.0 0.497158 0.496851 0.502532 0.496851 G C GC IISNP227 GC NaN AVBlank2-Nov-10-15 0.997000 0.999382 True 0.000182 0.496976 Recipient Hetero
AVBlank2-Nov-10-15 537.0 288.0 CYC10Nov2015Pool3 aIISNP102 IISNP102 chr1 154744807.0 C G 5654.0 5835.0 0.492123 0.507877 11489.0 11491.0 2.0 0.000174 chr1_154744236_154745348 572.0 0.492123 0.507789 0.492037 0.492037 G C GC IISNP102 GC NaN AVBlank2-Nov-10-15 1.414911 0.999826 True 0.000182 0.491941 Recipient Hetero
AVBlank2-Nov-10-15 538.0 288.0 CYC10Nov2015Pool3 aIISNP3 IISNP3 chr1 160786670.0 A G 15649.0 8.0 0.999489 0.000511 15657.0 15659.0 2.0 0.000128 chr1_160786113_160787219 558.0 0.000511 0.000511 0.999361 0.000511 A G AG IISNP3 AG NaN AVBlank2-Nov-10-15 1.928125 0.999872 True 0.001456 -0.000945 Recipient Homo
AVBlank2-Nov-10-15 539.0 288.0 CYC10Nov2015Pool3 aIISNP214 IISNP214 chr1 161019040.0 G C 4071.0 4349.0 0.483492 0.516508 8420.0 8424.0 4.0 0.000475 chr1_161018464_161019586 577.0 0.483492 0.516263 0.483262 0.483262 C G CG IISNP214 CG NaN AVBlank2-Nov-10-15 1.037265 0.999525 True 0.000187 0.483305 Recipient Hetero
AVBlank2-Nov-10-15 540.0 288.0 CYC10Nov2015Pool3 aIISNP242 IISNP242 chr1 179876988.0 C G 3.0 21134.0 0.000142 0.999858 21137.0 21139.0 2.0 0.000095 chr1_179876419_179877532 570.0 0.000142 0.999763 0.000142 0.000142 G C GC IISNP242 GC NaN AVBlank2-Nov-10-15 2.602889 0.999905 True 0.000182 -0.000040 Recipient Homo
AVBlank2-Nov-10-15 541.0 288.0 CYC10Nov2015Pool3 aIISNP264 IISNP264 chr1 205554085.0 G C 6.0 13262.0 0.000452 0.999548 13268.0 13280.0 12.0 0.000904 chr1_205553518_205554618 568.0 0.000452 0.998645 0.000452 0.000452 C G CG IISNP264 CG NaN AVBlank2-Nov-10-15 1.635194 0.999096 True 0.000187 0.000265 Recipient Homo
AVBlank2-Nov-10-15 542.0 288.0 CYC10Nov2015Pool3 aIISNP257 IISNP257 chr1 214837110.0 C G 6.0 8807.0 0.000681 0.999319 8813.0 8813.0 0.0 0.000000 chr1_214836531_214837646 580.0 0.000681 0.999319 0.000681 0.000681 G C GC IISNP257 GC NaN AVBlank2-Nov-10-15 1.085163 1.000000 True 0.000182 0.000499 Recipient Homo
AVBlank2-Nov-10-15 628.0 288.0 CYC10Nov2015Pool3 aIISNP82 IISNP82 chr17 80461935.0 C T 568.0 1614.0 0.260312 0.739688 2182.0 2184.0 2.0 0.000916 chr17_80461344_80462465 592.0 0.260312 0.739011 0.260073 0.260073 T C TC IISNP82 TC NaN AVBlank2-Nov-10-15 0.268920 0.999084 True 0.001475 0.258836 Recipient Hetero
AVBlank2-Nov-10-15 629.0 288.0 CYC10Nov2015Pool3 aIISNP51 IISNP51 chr17 80526139.0 A G 796.0 469.0 0.629249 0.370751 1265.0 1265.0 0.0 0.000000 chr17_80525564_80526669 576.0 0.370751 0.370751 0.629249 0.370751 A G AG IISNP51 AG NaN AVBlank2-Nov-10-15 0.155762 1.000000 True 0.001456 0.369295 Recipient Hetero
AVBlank2-Nov-10-15 630.0 288.0 CYC10Nov2015Pool3 aIISNP66 IISNP66 chr17 80531643.0 C G 4124.0 1765.0 0.700289 0.299711 5889.0 5892.0 3.0 0.000509 chr17_80531082_80532207 562.0 0.299711 0.299559 0.699932 0.299559 C G CG IISNP66 CG NaN AVBlank2-Nov-10-15 0.725494 0.999491 True 0.000187 0.299524 Recipient Hetero
AVBlank2-Nov-10-15 631.0 288.0 CYC10Nov2015Pool3 aIISNP74 IISNP74 chr17 80715702.0 G C 10449.0 6.0 0.999426 0.000574 10455.0 10456.0 1.0 0.000096 chr17_80715140_80716246 563.0 0.000574 0.000574 0.999331 0.000574 G C GC IISNP74 GC NaN AVBlank2-Nov-10-15 1.287469 0.999904 True 0.000182 0.000392 Recipient Homo
AVBlank2-Nov-10-15 632.0 288.0 CYC10Nov2015Pool3 aIISNP52 IISNP52 chr17 80765788.0 T C 8951.0 2.0 0.999777 0.000223 8953.0 8959.0 6.0 0.000670 chr17_80765219_80766321 570.0 0.000223 0.000223 0.999107 0.000223 T C TC IISNP52 TC NaN AVBlank2-Nov-10-15 1.103140 0.999330 True 0.001475 -0.001252 Recipient Homo
AVBlank2-Nov-10-15 633.0 288.0 CYC10Nov2015Pool3 aIISNP92 IISNP92 chr18 9749879.0 G A 6244.0 6598.0 0.486217 0.513783 12842.0 12847.0 5.0 0.000389 chr18_9749309_9750416 571.0 0.486217 0.513583 0.486028 0.486028 A G AG IISNP92 AG NaN AVBlank2-Nov-10-15 1.581878 0.999611 True 0.001456 0.484761 Recipient Hetero
AVBlank2-Nov-10-15 634.0 288.0 CYC10Nov2015Pool3 aIISNP87 IISNP87 chr18 29311034.0 G A 3268.0 3907.0 0.455470 0.544530 7175.0 7175.0 0.0 0.000000 chr18_29310484_29311587 551.0 0.455470 0.544530 0.455470 0.455470 A G AG IISNP87 AG NaN AVBlank2-Nov-10-15 0.883473 1.000000 True 0.001456 0.454014 Recipient Hetero
AVBlank2-Nov-10-15 635.0 288.0 CYC10Nov2015Pool3 aIISNP186 IISNP186 chr18 44561100.0 C G 3709.0 4277.0 0.464438 0.535562 7986.0 7989.0 3.0 0.000376 chr18_44560549_44561667 552.0 0.464438 0.535361 0.464263 0.464263 G C GC IISNP186 GC NaN AVBlank2-Nov-10-15 0.983702 0.999624 True 0.000182 0.464256 Recipient Hetero
AVBlank2-Nov-10-15 636.0 288.0 CYC10Nov2015Pool3 aIISNP69 IISNP69 chr18 47371014.0 C G 9.0 10479.0 0.000858 0.999142 10488.0 10490.0 2.0 0.000191 chr18_47370442_47371541 573.0 0.000858 0.998951 0.000858 0.000858 G C GC IISNP69 GC NaN AVBlank2-Nov-10-15 1.291655 0.999809 True 0.000182 0.000676 Recipient Homo
AVBlank2-Nov-10-15 637.0 288.0 CYC10Nov2015Pool3 aIISNP232 IISNP232 chr18 48333203.0 C G 6398.0 3.0 0.999531 0.000469 6401.0 6493.0 92.0 0.014169 chr18_48332670_48333785 534.0 0.000469 0.000462 0.985369 0.000462 C G CG IISNP232 CG NaN AVBlank2-Nov-10-15 0.799497 0.985831 True 0.000187 0.000282 Recipient Homo
AVBlank2-Nov-10-15 638.0 288.0 CYC10Nov2015Pool3 aIISNP41 IISNP41 chr18 55225777.0 T C 15.0 9880.0 0.001516 0.998484 9895.0 9895.0 0.0 0.000000 chr18_55225209_55226308 569.0 0.001516 0.998484 0.001516 0.001516 C T CT IISNP41 CT NaN AVBlank2-Nov-10-15 1.218392 1.000000 True 0.000984 0.000532 Recipient Homo
AVBlank2-Nov-10-15 639.0 288.0 CYC10Nov2015Pool3 aIISNP211 IISNP211 chr18 56204945.0 C G 5634.0 7166.0 0.440156 0.559844 12800.0 12805.0 5.0 0.000390 chr18_56204367_56205474 579.0 0.440156 0.559625 0.439984 0.439984 G C GC IISNP211 GC NaN AVBlank2-Nov-10-15 1.576706 0.999610 True 0.000182 0.439974 Recipient Hetero
AVBlank2-Nov-10-15 543.0 288.0 CYC10Nov2015Pool3 aIISNP19 IISNP19 chr1 233448413.0 C T 4036.0 3672.0 0.523612 0.476388 7708.0 7708.0 0.0 0.000000 chr1_233447873_233448982 541.0 0.476388 0.476388 0.523612 0.476388 C T CT IISNP19 CT NaN AVBlank2-Nov-10-15 0.949102 1.000000 True 0.000984 0.475404 Recipient Hetero
AVBlank2-Nov-10-15 544.0 288.0 CYC10Nov2015Pool3 aIISNP238 IISNP238 chr1 234041422.0 G C 3.0 9249.0 0.000324 0.999676 9252.0 9252.0 0.0 0.000000 chr1_234040863_234041981 560.0 0.000324 0.999676 0.000324 0.000324 C G CG IISNP238 CG NaN AVBlank2-Nov-10-15 1.139218 1.000000 True 0.000187 0.000137 Recipient Homo
AVBlank2-Nov-10-15 545.0 288.0 CYC10Nov2015Pool3 aIISNP104 IISNP104 chr1 236381825.0 G C 3316.0 0.0 1.000000 0.000000 3316.0 3316.0 0.0 0.000000 chr1_236381266_236382387 560.0 0.000000 0.000000 1.000000 0.000000 G C GC IISNP104 GC NaN AVBlank2-Nov-10-15 0.408306 1.000000 True 0.000182 -0.000182 Recipient Homo
AVBlank2-Nov-10-15 546.0 288.0 CYC10Nov2015Pool3 aIISNP83 IISNP83 chr1 239881926.0 A G 8857.0 2.0 0.999774 0.000226 8859.0 8863.0 4.0 0.000451 chr1_239881353_239882471 574.0 0.000226 0.000226 0.999323 0.000226 A G AG IISNP83 AG NaN AVBlank2-Nov-10-15 1.091320 0.999549 True 0.001456 -0.001230 Recipient Homo
AVBlank2-Nov-10-15 734.0 288.0 CYC10Nov2015Pool3 aIISNP60 IISNP60 chr5 178690725.0 G A 9014.0 17.0 0.998118 0.001882 9031.0 9031.0 0.0 0.000000 chr5_178690152_178691259 574.0 0.001882 0.001882 0.998118 0.001882 G A GA IISNP60 GA NaN AVBlank2-Nov-10-15 1.112006 1.000000 True 0.000987 0.000895 Recipient Homo
AVBlank2-Nov-10-15 735.0 288.0 CYC10Nov2015Pool3 aIISNP225 IISNP225 chr5 180046344.0 G C 0.0 1454.0 0.000000 1.000000 1454.0 1454.0 0.0 0.000000 chr5_180045793_180046900 552.0 0.000000 1.000000 0.000000 0.000000 C G CG IISNP225 CG NaN AVBlank2-Nov-10-15 0.179034 1.000000 True 0.000187 -0.000187 Recipient Homo
AVBlank2-Nov-10-15 736.0 288.0 CYC10Nov2015Pool3 aIISNP32 IISNP32 chr6 12059954.0 G A 3511.0 3197.0 0.523405 0.476595 6708.0 6712.0 4.0 0.000596 chr6_12059397_12060504 558.0 0.476595 0.476311 0.523093 0.476311 G A GA IISNP32 GA NaN AVBlank2-Nov-10-15 0.826462 0.999404 True 0.000987 0.475608 Recipient Hetero
AVBlank2-Nov-10-15 640.0 288.0 CYC10Nov2015Pool3 aIISNP130 IISNP130 chr19 619021.0 G C 254.0 0.0 1.000000 0.000000 254.0 254.0 0.0 0.000000 chr19_618466_619585 556.0 0.000000 0.000000 1.000000 0.000000 G C GC IISNP130 GC NaN AVBlank2-Nov-10-15 0.031276 1.000000 False NaN NaN NaN
AVBlank2-Nov-10-15 641.0 288.0 CYC10Nov2015Pool3 aIISNP226 IISNP226 chr19 7986638.0 C G 0.0 1088.0 0.000000 1.000000 1088.0 1088.0 0.0 0.000000 chr19_7986080_7987202 559.0 0.000000 1.000000 0.000000 0.000000 G C GC IISNP226 GC NaN AVBlank2-Nov-10-15 0.133968 1.000000 True 0.000182 -0.000182 Recipient Homo
AVBlank2-Nov-10-15 642.0 288.0 CYC10Nov2015Pool3 aIISNP159 IISNP159 chr19 10084292.0 C G 4315.0 4.0 0.999074 0.000926 4319.0 4322.0 3.0 0.000694 chr19_10083723_10084832 570.0 0.000926 0.000925 0.998380 0.000925 C G CG IISNP159 CG NaN AVBlank2-Nov-10-15 0.532177 0.999306 True 0.000187 0.000739 Recipient Homo
AVBlank2-Nov-10-15 643.0 288.0 CYC10Nov2015Pool3 aIISNP100 IISNP100 chr19 10600442.0 G C 3334.0 3118.0 0.516739 0.483261 6452.0 6455.0 3.0 0.000465 chr19_10599851_10600965 592.0 0.483261 0.483036 0.516499 0.483036 G C GC IISNP100 GC NaN AVBlank2-Nov-10-15 0.794818 0.999535 True 0.000182 0.483079 Recipient Hetero
AVBlank2-Nov-10-15 644.0 288.0 CYC10Nov2015Pool3 aIISNP217 IISNP217 chr19 10670184.0 C G 39.0 65.0 0.375000 0.625000 104.0 104.0 0.0 0.000000 chr19_10669614_10670743 571.0 0.375000 0.625000 0.375000 0.375000 G C GC IISNP217 GC NaN AVBlank2-Nov-10-15 0.012806 1.000000 False NaN NaN NaN
AVBlank2-Nov-10-15 645.0 288.0 CYC10Nov2015Pool3 aIISNP274 IISNP274 chr19 18377647.0 G C 1136.0 1393.0 0.449189 0.550811 2529.0 2536.0 7.0 0.002760 chr19_18377056_18378185 592.0 0.449189 0.549290 0.447950 0.447950 C G CG IISNP274 CG NaN AVBlank2-Nov-10-15 0.312263 0.997240 True 0.000187 0.449002 Recipient Hetero
AVBlank2-Nov-10-15 646.0 288.0 CYC10Nov2015Pool3 aIISNP171 IISNP171 chr19 36278470.0 C G 113.0 0.0 1.000000 0.000000 113.0 113.0 0.0 0.000000 chr19_36277889_36279010 582.0 0.000000 0.000000 1.000000 0.000000 C G CG IISNP171 CG NaN AVBlank2-Nov-10-15 0.013914 1.000000 False NaN NaN NaN
AVBlank2-Nov-10-15 647.0 288.0 CYC10Nov2015Pool3 aIISNP13 IISNP13 chr19 39559807.0 A C 7381.0 6094.0 0.547755 0.452245 13475.0 13482.0 7.0 0.000519 chr19_39559236_39560337 572.0 0.452245 0.452010 0.547471 0.452010 A C AC IISNP13 AC NaN AVBlank2-Nov-10-15 1.660067 0.999481 True 0.000181 0.452064 Recipient Hetero
AVBlank2-Nov-10-15 648.0 288.0 CYC10Nov2015Pool3 aIISNP95 IISNP95 chr19 41939297.0 C G 2404.0 2519.0 0.488320 0.511680 4923.0 4927.0 4.0 0.000812 chr19_41938759_41939869 539.0 0.488320 0.511264 0.487924 0.487924 G C GC IISNP95 GC NaN AVBlank2-Nov-10-15 0.606672 0.999188 True 0.000182 0.488138 Recipient Hetero
AVBlank2-Nov-10-15 649.0 288.0 CYC10Nov2015Pool3 aIISNP117 IISNP117 chr19 44303066.0 C G 752.0 1366.0 0.355052 0.644948 2118.0 2120.0 2.0 0.000943 chr19_44302506_44303626 561.0 0.355052 0.644340 0.354717 0.354717 G C GC IISNP117 GC NaN AVBlank2-Nov-10-15 0.261040 0.999057 True 0.000182 0.354870 Recipient Hetero
AVBlank2-Nov-10-15 650.0 288.0 CYC10Nov2015Pool3 aIISNP136 IISNP136 chr19 44981883.0 C G 4728.0 11.0 0.997679 0.002321 4739.0 4741.0 2.0 0.000422 chr19_44981323_44982437 561.0 0.002321 0.002320 0.997258 0.002320 C G CG IISNP136 CG NaN AVBlank2-Nov-10-15 0.583769 0.999578 True 0.000187 0.002134 Recipient Homo
AVBlank2-Nov-10-15 651.0 288.0 CYC10Nov2015Pool3 aIISNP126 IISNP126 chr19 48621036.0 C G 10732.0 9512.0 0.530132 0.469868 20244.0 20265.0 21.0 0.001036 chr19_48620482_48621601 555.0 0.469868 0.469381 0.529583 0.469381 C G CG IISNP126 CG NaN AVBlank2-Nov-10-15 2.495271 0.998964 True 0.000187 0.469681 Recipient Hetero
AVBlank2-Nov-10-15 652.0 288.0 CYC10Nov2015Pool3 aIISNP218 IISNP218 chr19 52115645.0 G C 0.0 5036.0 0.000000 1.000000 5036.0 5036.0 0.0 0.000000 chr19_52115107_52116208 539.0 0.000000 1.000000 0.000000 0.000000 C G CG IISNP218 CG NaN AVBlank2-Nov-10-15 0.620093 1.000000 True 0.000187 -0.000187 Recipient Homo
AVBlank2-Nov-10-15 653.0 288.0 CYC10Nov2015Pool3 aIISNP190 IISNP190 chr19 53344118.0 C G 6.0 12280.0 0.000488 0.999512 12286.0 12288.0 2.0 0.000163 chr19_53343564_53344688 555.0 0.000488 0.999349 0.000488 0.000488 G C GC IISNP190 GC NaN AVBlank2-Nov-10-15 1.513047 0.999837 True 0.000182 0.000306 Recipient Homo
AVBlank2-Nov-10-15 654.0 288.0 CYC10Nov2015Pool3 aIISNP199 IISNP199 chr19 54664209.0 G C 9934.0 8.0 0.999195 0.000805 9942.0 9942.0 0.0 0.000000 chr19_54663644_54664769 566.0 0.000805 0.000805 0.999195 0.000805 G C GC IISNP199 GC NaN AVBlank2-Nov-10-15 1.224179 1.000000 True 0.000182 0.000623 Recipient Homo
AVBlank2-Nov-10-15 737.0 288.0 CYC10Nov2015Pool3 aIISNP279 IISNP279 chr6 26509330.0 C G 8385.0 5818.0 0.590368 0.409632 14203.0 14211.0 8.0 0.000563 chr6_26508757_26509875 574.0 0.409632 0.409401 0.590036 0.409401 C G CG IISNP279 CG NaN AVBlank2-Nov-10-15 1.749830 0.999437 True 0.000187 0.409445 Recipient Hetero
AVBlank2-Nov-10-15 738.0 288.0 CYC10Nov2015Pool3 aIISNP261 IISNP261 chr6 36287312.0 G C 3768.0 3450.0 0.522028 0.477972 7218.0 7218.0 0.0 0.000000 chr6_36286765_36287879 548.0 0.477972 0.477972 0.522028 0.477972 G C GC IISNP261 GC NaN AVBlank2-Nov-10-15 0.888767 1.000000 True 0.000182 0.477790 Recipient Hetero
AVBlank2-Nov-10-15 739.0 288.0 CYC10Nov2015Pool3 aIISNP134 IISNP134 chr6 38781866.0 C G 2045.0 2724.0 0.428811 0.571189 4769.0 4769.0 0.0 0.000000 chr6_38781300_38782411 567.0 0.428811 0.571189 0.428811 0.428811 G C GC IISNP134 GC NaN AVBlank2-Nov-10-15 0.587217 1.000000 True 0.000182 0.428629 Recipient Hetero
AVBlank2-Nov-10-15 740.0 288.0 CYC10Nov2015Pool3 aIISNP144 IISNP144 chr6 41773576.0 G C 872.0 9634.0 0.083000 0.917000 10506.0 10515.0 9.0 0.000856 chr6_41773010_41774136 567.0 0.083000 0.916215 0.082929 0.082929 C G CG IISNP144 CG NaN AVBlank2-Nov-10-15 1.294734 0.999144 True 0.000187 0.082813 Recipient Homo
AVBlank2-Nov-10-15 741.0 288.0 CYC10Nov2015Pool3 aIISNP263 IISNP263 chr6 46107752.0 C G 14853.0 37.0 0.997515 0.002485 14890.0 14895.0 5.0 0.000336 chr6_46107197_46108304 556.0 0.002485 0.002484 0.997180 0.002484 C G CG IISNP263 CG NaN AVBlank2-Nov-10-15 1.834052 0.999664 True 0.000187 0.002298 Recipient Homo
AVBlank2-Nov-10-15 742.0 288.0 CYC10Nov2015Pool3 aIISNP143 IISNP143 chr6 52617731.0 C G 2202.0 1896.0 0.537335 0.462665 4098.0 4098.0 0.0 0.000000 chr6_52617161_52618275 571.0 0.462665 0.462665 0.537335 0.462665 C G CG IISNP143 CG NaN AVBlank2-Nov-10-15 0.504595 1.000000 True 0.000187 0.462478 Recipient Hetero
AVBlank2-Nov-10-15 743.0 288.0 CYC10Nov2015Pool3 aIISNP56 IISNP56 chr6 55155704.0 C A 34.0 10933.0 0.003100 0.996900 10967.0 10967.0 0.0 0.000000 chr6_55155134_55156239 571.0 0.003100 0.996900 0.003100 0.003100 A C AC IISNP56 AC NaN AVBlank2-Nov-10-15 1.350389 1.000000 True 0.000181 0.002919 Recipient Homo
AVBlank2-Nov-10-15 744.0 288.0 CYC10Nov2015Pool3 aIISNP246 IISNP246 chr6 56482801.0 C G 17804.0 5.0 0.999719 0.000281 17809.0 17811.0 2.0 0.000112 chr6_56482232_56483352 570.0 0.000281 0.000281 0.999607 0.000281 C G CG IISNP246 CG NaN AVBlank2-Nov-10-15 2.193105 0.999888 True 0.000187 0.000094 Recipient Homo
AVBlank2-Nov-10-15 745.0 288.0 CYC10Nov2015Pool3 aIISNP237 IISNP237 chr6 74073531.0 C G 6353.0 2.0 0.999685 0.000315 6355.0 6361.0 6.0 0.000943 chr6_74072980_74074097 552.0 0.000315 0.000314 0.998742 0.000314 C G CG IISNP237 CG NaN AVBlank2-Nov-10-15 0.783243 0.999057 True 0.000187 0.000128 Recipient Homo
AVBlank2-Nov-10-15 746.0 288.0 CYC10Nov2015Pool3 aIISNP202 IISNP202 chr6 76660551.0 G C 13352.0 4.0 0.999701 0.000299 13356.0 13356.0 0.0 0.000000 chr6_76659989_76661118 563.0 0.000299 0.000299 0.999701 0.000299 G C GC IISNP202 GC NaN AVBlank2-Nov-10-15 1.644552 1.000000 True 0.000182 0.000117 Recipient Homo
AVBlank2-Nov-10-15 747.0 288.0 CYC10Nov2015Pool3 aIISNP36 IISNP36 chr6 120560694.0 T A 6.0 4146.0 0.001445 0.998555 4152.0 4154.0 2.0 0.000481 chr6_120560128_120561231 567.0 0.001445 0.998074 0.001444 0.001444 A T AT IISNP36 AT NaN AVBlank2-Nov-10-15 0.511491 0.999519 True 0.000350 0.001095 Recipient Homo
AVBlank2-Nov-10-15 748.0 288.0 CYC10Nov2015Pool3 aIISNP34 IISNP34 chr6 123894978.0 C A 0.0 785.0 0.000000 1.000000 785.0 785.0 0.0 0.000000 chr6_123894407_123895512 572.0 0.000000 1.000000 0.000000 0.000000 A C AC IISNP34 AC NaN AVBlank2-Nov-10-15 0.096659 1.000000 False NaN NaN NaN
AVBlank2-Nov-10-15 749.0 288.0 CYC10Nov2015Pool3 aIISNP164 IISNP164 chr6 126278230.0 G C 11355.0 13.0 0.998856 0.001144 11368.0 11371.0 3.0 0.000264 chr6_126277677_126278784 554.0 0.001144 0.001143 0.998593 0.001143 G C GC IISNP164 GC NaN AVBlank2-Nov-10-15 1.400135 0.999736 True 0.000182 0.000962 Recipient Homo
AVBlank2-Nov-10-15 750.0 288.0 CYC10Nov2015Pool3 aIISNP54 IISNP54 chr6 127463376.0 C A 1379.0 1063.0 0.564701 0.435299 2442.0 2442.0 0.0 0.000000 chr6_127462805_127463913 572.0 0.435299 0.435299 0.564701 0.435299 C A CA IISNP54 CA NaN AVBlank2-Nov-10-15 0.300689 1.000000 True 0.000474 0.434824 Recipient Hetero
AVBlank2-Nov-10-15 751.0 288.0 CYC10Nov2015Pool3 aIISNP247 IISNP247 chr6 138413333.0 G C 5953.0 6431.0 0.480701 0.519299 12384.0 12411.0 27.0 0.002175 chr6_138412785_138413907 549.0 0.480701 0.518169 0.479655 0.479655 C G CG IISNP247 CG NaN AVBlank2-Nov-10-15 1.528192 0.997825 True 0.000187 0.480514 Recipient Hetero
AVBlank2-Nov-10-15 752.0 288.0 CYC10Nov2015Pool3 aIISNP50 IISNP50 chr6 148761456.0 G C 11051.0 7268.0 0.603253 0.396747 18319.0 18331.0 12.0 0.000655 chr6_148760890_148761999 567.0 0.396747 0.396487 0.602859 0.396487 G C GC IISNP50 GC NaN AVBlank2-Nov-10-15 2.257134 0.999345 True 0.000182 0.396565 Recipient Hetero
AVBlank2-Nov-10-15 753.0 288.0 CYC10Nov2015Pool3 aIISNP172 IISNP172 chr6 150209717.0 C G 293.0 241.0 0.548689 0.451311 534.0 534.0 0.0 0.000000 chr6_150209159_150210278 559.0 0.451311 0.451311 0.548689 0.451311 C G CG IISNP172 CG NaN AVBlank2-Nov-10-15 0.065753 1.000000 False NaN NaN NaN
AVBlank2-Nov-10-15 754.0 288.0 CYC10Nov2015Pool3 aIISNP45 IISNP45 chr6 152697706.0 C T 5591.0 4933.0 0.531262 0.468738 10524.0 10524.0 0.0 0.000000 chr6_152697130_152698240 577.0 0.468738 0.468738 0.531262 0.468738 C T CT IISNP45 CT NaN AVBlank2-Nov-10-15 1.295842 1.000000 True 0.000984 0.467754 Recipient Hetero
AVBlank2-Nov-10-15 755.0 288.0 CYC10Nov2015Pool3 aIISNP122 IISNP122 chr6 170862300.0 G C 7025.0 4267.0 0.622122 0.377878 11292.0 11296.0 4.0 0.000354 chr6_170861722_170862832 579.0 0.377878 0.377744 0.621902 0.377744 G C GC IISNP122 GC NaN AVBlank2-Nov-10-15 1.390900 0.999646 True 0.000182 0.377696 Recipient Hetero
AVBlank2-Nov-10-15 756.0 288.0 CYC10Nov2015Pool3 aIISNP267 IISNP267 chr7 4026944.0 C G 9141.0 39.0 0.995752 0.004248 9180.0 9228.0 48.0 0.005202 chr7_4026399_4027521 546.0 0.004248 0.004226 0.990572 0.004226 C G CG IISNP267 CG NaN AVBlank2-Nov-10-15 1.136263 0.994798 True 0.000187 0.004061 Recipient Homo
AVBlank2-Nov-10-15 547.0 288.0 CYC10Nov2015Pool3 aIISNP131 IISNP131 chr1 247752019.0 G C 3678.0 3.0 0.999185 0.000815 3681.0 3682.0 1.0 0.000272 chr1_247751483_247752601 537.0 0.000815 0.000815 0.998914 0.000815 G C GC IISNP131 GC NaN AVBlank2-Nov-10-15 0.453372 0.999728 True 0.000182 0.000633 Recipient Homo
AVBlank2-Nov-10-15 548.0 288.0 CYC10Nov2015Pool3 aIISNP121 IISNP121 chr10 5136651.0 C G 3361.0 3800.0 0.469348 0.530652 7161.0 7162.0 1.0 0.000140 chr10_5136059_5137186 593.0 0.469348 0.530578 0.469282 0.469282 G C GC IISNP121 GC NaN AVBlank2-Nov-10-15 0.881872 0.999860 True 0.000182 0.469166 Recipient Hetero
AVBlank2-Nov-10-15 549.0 288.0 CYC10Nov2015Pool3 aIISNP244 IISNP244 chr10 21414892.0 C G 8435.0 3.0 0.999644 0.000356 8438.0 8441.0 3.0 0.000355 chr10_21414322_21415442 571.0 0.000356 0.000355 0.999289 0.000355 C G CG IISNP244 CG NaN AVBlank2-Nov-10-15 1.039358 0.999645 True 0.000187 0.000169 Recipient Homo
AVBlank2-Nov-10-15 550.0 288.0 CYC10Nov2015Pool3 aIISNP114 IISNP114 chr10 24873369.0 C G 2591.0 2917.0 0.470407 0.529593 5508.0 5728.0 220.0 0.038408 chr10_24872787_24873906 583.0 0.470407 0.509253 0.452339 0.452339 G C GC IISNP114 GC NaN AVBlank2-Nov-10-15 0.705301 0.961592 True 0.000182 0.470225 Recipient Hetero
AVBlank2-Nov-10-15 551.0 288.0 CYC10Nov2015Pool3 aIISNP178 IISNP178 chr10 25701341.0 C G 2.0 3895.0 0.000513 0.999487 3897.0 3897.0 0.0 0.000000 chr10_25700758_25701869 584.0 0.000513 0.999487 0.000513 0.000513 G C GC IISNP178 GC NaN AVBlank2-Nov-10-15 0.479846 1.000000 True 0.000182 0.000331 Recipient Homo
AVBlank2-Nov-10-15 552.0 288.0 CYC10Nov2015Pool3 aIISNP181 IISNP181 chr10 38344700.0 C G 5960.0 222.0 0.964089 0.035911 6182.0 6198.0 16.0 0.002581 chr10_38344113_38345242 588.0 0.035911 0.035818 0.961601 0.035818 C G CG IISNP181 CG NaN AVBlank2-Nov-10-15 0.763173 0.997419 True 0.000187 0.035724 Recipient Homo
AVBlank2-Nov-10-15 553.0 288.0 CYC10Nov2015Pool3 aIISNP215 IISNP215 chr10 69934258.0 C G 2879.0 2771.0 0.509558 0.490442 5650.0 5655.0 5.0 0.000884 chr10_69933675_69934782 584.0 0.490442 0.490009 0.509107 0.490009 C G CG IISNP215 CG NaN AVBlank2-Nov-10-15 0.696312 0.999116 True 0.000187 0.490256 Recipient Hetero
AVBlank2-Nov-10-15 554.0 288.0 CYC10Nov2015Pool3 aIISNP165 IISNP165 chr10 90342837.0 C G 3640.0 2446.0 0.598094 0.401906 6086.0 6086.0 0.0 0.000000 chr10_90342263_90343376 575.0 0.401906 0.401906 0.598094 0.401906 C G CG IISNP165 CG NaN AVBlank2-Nov-10-15 0.749382 1.000000 True 0.000187 0.401719 Recipient Hetero
AVBlank2-Nov-10-15 555.0 288.0 CYC10Nov2015Pool3 aIISNP35 IISNP35 chr10 97172595.0 T C 6102.0 6577.0 0.481268 0.518732 12679.0 12679.0 0.0 0.000000 chr10_97172060_97173166 536.0 0.481268 0.518732 0.481268 0.481268 C T CT IISNP35 CT NaN AVBlank2-Nov-10-15 1.561192 1.000000 True 0.000984 0.480284 Recipient Hetero
AVBlank2-Nov-10-15 556.0 288.0 CYC10Nov2015Pool3 aIISNP154 IISNP154 chr10 99439541.0 G C 8472.0 6.0 0.999292 0.000708 8478.0 8480.0 2.0 0.000236 chr10_99438974_99440086 568.0 0.000708 0.000708 0.999057 0.000708 G C GC IISNP154 GC NaN AVBlank2-Nov-10-15 1.044160 0.999764 True 0.000182 0.000526 Recipient Homo
AVBlank2-Nov-10-15 557.0 288.0 CYC10Nov2015Pool3 aIISNP256 IISNP256 chr10 114053546.0 C G 0.0 623.0 0.000000 1.000000 623.0 623.0 0.0 0.000000 chr10_114052989_114054096 558.0 0.000000 1.000000 0.000000 0.000000 G C GC IISNP256 GC NaN AVBlank2-Nov-10-15 0.076711 1.000000 False NaN NaN NaN
AVBlank2-Nov-10-15 558.0 288.0 CYC10Nov2015Pool3 aIISNP189 IISNP189 chr10 126714714.0 G C 3760.0 3.0 0.999203 0.000797 3763.0 3765.0 2.0 0.000531 chr10_126714134_126715248 581.0 0.000797 0.000797 0.998672 0.000797 G C GC IISNP189 GC NaN AVBlank2-Nov-10-15 0.463592 0.999469 True 0.000182 0.000615 Recipient Homo
AVBlank2-Nov-10-15 559.0 288.0 CYC10Nov2015Pool3 aIISNP204 IISNP204 chr10 128019025.0 C G 12652.0 7194.0 0.637509 0.362491 19846.0 19849.0 3.0 0.000151 chr10_128018457_128019577 569.0 0.362491 0.362436 0.637412 0.362436 C G CG IISNP204 CG NaN AVBlank2-Nov-10-15 2.444049 0.999849 True 0.000187 0.362304 Recipient Hetero
AVBlank2-Nov-10-15 560.0 288.0 CYC10Nov2015Pool3 aIISNP110 IISNP110 chr10 129899778.0 G C 7941.0 1232.0 0.865693 0.134307 9173.0 9174.0 1.0 0.000109 chr10_129899187_129900315 592.0 0.134307 0.134293 0.865598 0.134293 G C GC IISNP110 GC NaN AVBlank2-Nov-10-15 1.129614 0.999891 True 0.000182 0.134125 Recipient Hetero
AVBlank2-Nov-10-15 561.0 288.0 CYC10Nov2015Pool3 aIISNP239 IISNP239 chr11 299411.0 C G 1225.0 863.0 0.586686 0.413314 2088.0 2088.0 0.0 0.000000 chr11_298837_299939 575.0 0.413314 0.413314 0.586686 0.413314 C G CG IISNP239 CG NaN AVBlank2-Nov-10-15 0.257100 1.000000 True 0.000187 0.413127 Recipient Hetero
AVBlank2-Nov-10-15 562.0 288.0 CYC10Nov2015Pool3 aIISNP187 IISNP187 chr11 4567335.0 C G 8.0 8182.0 0.000977 0.999023 8190.0 8190.0 0.0 0.000000 chr11_4566780_4567909 556.0 0.000977 0.999023 0.000977 0.000977 G C GC IISNP187 GC NaN AVBlank2-Nov-10-15 1.008452 1.000000 True 0.000182 0.000795 Recipient Homo
AVBlank2-Nov-10-15 563.0 288.0 CYC10Nov2015Pool3 aIISNP25 IISNP25 chr11 5098714.0 C T 5092.0 10.0 0.998040 0.001960 5102.0 5103.0 1.0 0.000196 chr11_5098168_5099267 547.0 0.001960 0.001960 0.997844 0.001960 C T CT IISNP25 CT NaN AVBlank2-Nov-10-15 0.628343 0.999804 True 0.000984 0.000976 Recipient Homo
AVBlank2-Nov-10-15 564.0 288.0 CYC10Nov2015Pool3 aIISNP24 IISNP24 chr11 5099393.0 T A 17359.0 6.0 0.999654 0.000346 17365.0 17374.0 9.0 0.000518 chr11_5098828_5099937 566.0 0.000346 0.000345 0.999137 0.000345 T A TA IISNP24 TA NaN AVBlank2-Nov-10-15 2.139297 0.999482 True 0.000269 0.000077 Recipient Homo
AVBlank2-Nov-10-15 565.0 288.0 CYC10Nov2015Pool3 aIISNP38 IISNP38 chr11 5709028.0 C T 8611.0 7628.0 0.530267 0.469733 16239.0 16239.0 0.0 0.000000 chr11_5708471_5709577 558.0 0.469733 0.469733 0.530267 0.469733 C T CT IISNP38 CT NaN AVBlank2-Nov-10-15 1.999542 1.000000 True 0.000984 0.468749 Recipient Hetero
AVBlank2-Nov-10-15 566.0 288.0 CYC10Nov2015Pool3 aIISNP206 IISNP206 chr11 8947283.0 G C 8.0 12119.0 0.000660 0.999340 12127.0 12127.0 0.0 0.000000 chr11_8946706_8947820 578.0 0.000660 0.999340 0.000660 0.000660 C G CG IISNP206 CG NaN AVBlank2-Nov-10-15 1.493223 1.000000 True 0.000187 0.000473 Recipient Homo
AVBlank2-Nov-10-15 567.0 288.0 CYC10Nov2015Pool3 aIISNP84 IISNP84 chr11 11096221.0 C T 11570.0 22.0 0.998102 0.001898 11592.0 11595.0 3.0 0.000259 chr11_11095660_11096769 562.0 0.001898 0.001897 0.997844 0.001897 C T CT IISNP84 CT NaN AVBlank2-Nov-10-15 1.427716 0.999741 True 0.000984 0.000914 Recipient Homo
AVBlank2-Nov-10-15 568.0 288.0 CYC10Nov2015Pool3 aIISNP109 IISNP109 chr11 11292700.0 G C 11586.0 0.0 1.000000 0.000000 11586.0 11589.0 3.0 0.000259 chr11_11292148_11293259 553.0 0.000000 0.000000 0.999741 0.000000 G C GC IISNP109 GC NaN AVBlank2-Nov-10-15 1.426978 0.999741 True 0.000182 -0.000182 Recipient Homo
AVBlank2-Nov-10-15 569.0 288.0 CYC10Nov2015Pool3 aIISNP107 IISNP107 chr11 17519742.0 C G 639.0 807.0 0.441909 0.558091 1446.0 1447.0 1.0 0.000691 chr11_17519170_17520279 573.0 0.441909 0.557706 0.441603 0.441603 G C GC IISNP107 GC NaN AVBlank2-Nov-10-15 0.178172 0.999309 True 0.000182 0.441727 Recipient Hetero
AVBlank2-Nov-10-15 655.0 288.0 CYC10Nov2015Pool3 aIISNP281 IISNP281 chr19 56423074.0 C G 10219.0 18.0 0.998242 0.001758 10237.0 10237.0 0.0 0.000000 chr19_56422500_56423625 575.0 0.001758 0.001758 0.998242 0.001758 C G CG IISNP281 CG NaN AVBlank2-Nov-10-15 1.260503 1.000000 True 0.000187 0.001571 Recipient Homo
AVBlank2-Nov-10-15 656.0 288.0 CYC10Nov2015Pool3 aIISNP94 IISNP94 chr19 57085769.0 G C 17665.0 2.0 0.999887 0.000113 17667.0 17671.0 4.0 0.000226 chr19_57085220_57086327 550.0 0.000113 0.000113 0.999660 0.000113 G C GC IISNP94 GC NaN AVBlank2-Nov-10-15 2.175867 0.999774 True 0.000182 -0.000069 Recipient Homo
AVBlank2-Nov-10-15 657.0 288.0 CYC10Nov2015Pool3 aIISNP248 IISNP248 chr19 57838018.0 C G 4.0 3500.0 0.001142 0.998858 3504.0 3507.0 3.0 0.000855 chr19_57837471_57838600 548.0 0.001142 0.998004 0.001141 0.001141 G C GC IISNP248 GC NaN AVBlank2-Nov-10-15 0.431824 0.999145 True 0.000182 0.000960 Recipient Homo
AVBlank2-Nov-10-15 658.0 288.0 CYC10Nov2015Pool3 aIISNP233 IISNP233 chr2 3469463.0 G C 15633.0 34.0 0.997830 0.002170 15667.0 15674.0 7.0 0.000447 chr2_3468916_3470030 548.0 0.002170 0.002169 0.997384 0.002169 G C GC IISNP233 GC NaN AVBlank2-Nov-10-15 1.929972 0.999553 True 0.000182 0.001988 Recipient Homo
AVBlank2-Nov-10-15 659.0 288.0 CYC10Nov2015Pool3 aIISNP28 IISNP28 chr2 10085722.0 G A 7279.0 16.0 0.997807 0.002193 7295.0 7295.0 0.0 0.000000 chr2_10085153_10086253 570.0 0.002193 0.002193 0.997807 0.002193 G A GA IISNP28 GA NaN AVBlank2-Nov-10-15 0.898248 1.000000 True 0.000987 0.001206 Recipient Homo
AVBlank2-Nov-10-15 660.0 288.0 CYC10Nov2015Pool3 aIISNP175 IISNP175 chr2 27324724.0 G C 0.0 6956.0 0.000000 1.000000 6956.0 6958.0 2.0 0.000287 chr2_27324182_27325292 543.0 0.000000 0.999713 0.000000 0.000000 C G CG IISNP175 CG NaN AVBlank2-Nov-10-15 0.856753 0.999713 True 0.000187 -0.000187 Recipient Homo
AVBlank2-Nov-10-15 661.0 288.0 CYC10Nov2015Pool3 aIISNP266 IISNP266 chr2 28824793.0 C G 4.0 2.0 0.666667 0.333333 6.0 6.0 0.0 0.000000 chr2_28824241_28825363 553.0 0.333333 0.333333 0.666667 0.333333 C G CG IISNP266 CG NaN AVBlank2-Nov-10-15 0.000739 1.000000 False NaN NaN NaN
AVBlank2-Nov-10-15 662.0 288.0 CYC10Nov2015Pool3 aIISNP135 IISNP135 chr2 29416366.0 G C 5263.0 4317.0 0.549374 0.450626 9580.0 9581.0 1.0 0.000104 chr2_29415814_29416943 553.0 0.450626 0.450579 0.549316 0.450579 G C GC IISNP135 GC NaN AVBlank2-Nov-10-15 1.179728 0.999896 True 0.000182 0.450444 Recipient Hetero
AVBlank2-Nov-10-15 663.0 288.0 CYC10Nov2015Pool3 aIISNP148 IISNP148 chr2 75113789.0 C G 4538.0 4730.0 0.489642 0.510358 9268.0 9272.0 4.0 0.000431 chr2_75113219_75114341 571.0 0.489642 0.510138 0.489431 0.489431 G C GC IISNP148 GC NaN AVBlank2-Nov-10-15 1.141681 0.999569 True 0.000182 0.489460 Recipient Hetero
AVBlank2-Nov-10-15 757.0 288.0 CYC10Nov2015Pool3 aIISNP193 IISNP193 chr7 12269417.0 C G 2227.0 4.0 0.998207 0.001793 2231.0 2231.0 0.0 0.000000 chr7_12268849_12269978 569.0 0.001793 0.001793 0.998207 0.001793 C G CG IISNP193 CG NaN AVBlank2-Nov-10-15 0.274708 1.000000 True 0.000187 0.001606 Recipient Homo
AVBlank2-Nov-10-15 758.0 288.0 CYC10Nov2015Pool3 aIISNP22 IISNP22 chr7 13894276.0 A G 9.0 10227.0 0.000879 0.999121 10236.0 10238.0 2.0 0.000195 chr7_13893713_13894820 564.0 0.000879 0.998926 0.000879 0.000879 G A GA IISNP22 GA NaN AVBlank2-Nov-10-15 1.260626 0.999805 True 0.000987 -0.000108 Recipient Homo
AVBlank2-Nov-10-15 759.0 288.0 CYC10Nov2015Pool3 aIISNP203 IISNP203 chr7 20180717.0 C G 2.0 13616.0 0.000147 0.999853 13618.0 13622.0 4.0 0.000294 chr7_20180151_20181280 567.0 0.000147 0.999560 0.000147 0.000147 G C GC IISNP203 GC NaN AVBlank2-Nov-10-15 1.677305 0.999706 True 0.000182 -0.000035 Recipient Homo
AVBlank2-Nov-10-15 760.0 288.0 CYC10Nov2015Pool3 aIISNP185 IISNP185 chr7 25194665.0 G C 7505.0 2.0 0.999734 0.000266 7507.0 7511.0 4.0 0.000533 chr7_25194102_25195226 564.0 0.000266 0.000266 0.999201 0.000266 G C GC IISNP185 GC NaN AVBlank2-Nov-10-15 0.924845 0.999467 True 0.000182 0.000084 Recipient Homo
AVBlank2-Nov-10-15 761.0 288.0 CYC10Nov2015Pool3 aIISNP93 IISNP93 chr7 47925331.0 C G 7889.0 0.0 1.000000 0.000000 7889.0 7912.0 23.0 0.002907 chr7_47924777_47925902 555.0 0.000000 0.000000 0.997093 0.000000 C G CG IISNP93 CG NaN AVBlank2-Nov-10-15 0.974221 0.997093 True 0.000187 -0.000187 Recipient Homo
AVBlank2-Nov-10-15 762.0 288.0 CYC10Nov2015Pool3 aIISNP112 IISNP112 chr7 130021488.0 G C 2952.0 3045.0 0.492246 0.507754 5997.0 6006.0 9.0 0.001499 chr7_130020932_130022055 557.0 0.492246 0.506993 0.491508 0.491508 C G CG IISNP112 CG NaN AVBlank2-Nov-10-15 0.739531 0.998501 True 0.000187 0.492059 Recipient Hetero
AVBlank2-Nov-10-15 763.0 288.0 CYC10Nov2015Pool3 aIISNP166 IISNP166 chr7 138740037.0 G C 12231.0 15.0 0.998775 0.001225 12246.0 12246.0 0.0 0.000000 chr7_138739465_138740586 573.0 0.001225 0.001225 0.998775 0.001225 G C GC IISNP166 GC NaN AVBlank2-Nov-10-15 1.507875 1.000000 True 0.000182 0.001043 Recipient Homo

46847 rows × 35 columns

In [62]:
# help(pd.DataFrame.iplot)
In [60]:
SNP_cov
Out[60]:
Genome_location Ref_start_pos Ref_end_pos rsID SNP_pos_in_ref Ref Alt amp_length SNP_pos SNP_cov_end_bound SNP_cov_type
SNP_ID
IISNP1 chr11_115206646_115207761 501 616 rs10488710 chr11_115206646_115207761:531 C G 116 31 35 False
IISNP10 chr4_46329095_46330254 501 660 rs279844 chr4_46329095_46330254:561 A T 160 61 79 False
IISNP100 chr19_10599851_10600965 501 615 rs1048290 chr19_10599851_10600965:592 G C 115 92 34 False
IISNP101 chr17_33998221_33999330 501 610 rs1049379 chr17_33998221_33999330:582 G C 110 82 29 True
IISNP102 chr1_154744236_154745348 501 613 rs1051614 chr1_154744236_154745348:572 C G 113 72 32 True
IISNP103 chr2_118574685_118575803 501 619 rs1052637 chr2_118574685_118575803:531 C G 119 31 38 False
IISNP104 chr1_236381266_236382387 501 622 rs1055851 chr1_236381266_236382387:560 G C 122 60 41 True
IISNP105 chr20_24939035_24940159 501 625 rs1056033 chr20_24939035_24940159:556 G C 125 56 44 True
IISNP106 chr5_145441622_145442735 501 614 rs1056149 chr5_145441622_145442735:582 G C 114 82 33 True
IISNP107 chr11_17519170_17520279 501 610 rs1064074 chr11_17519170_17520279:573 C G 110 73 29 True
IISNP108 chr2_85769181_85770292 501 612 rs1078004 chr2_85769181_85770292:531 C G 112 31 31 False
IISNP109 chr11_11292148_11293259 501 612 rs10831567 chr11_11292148_11293259:553 G C 112 53 31 True
IISNP11 chr4_169663057_169664186 501 630 rs6811238 chr4_169663057_169664186:559 T G 130 59 49 True
IISNP110 chr10_129899187_129900315 501 629 rs11106 chr10_129899187_129900315:592 G C 129 92 48 False
IISNP111 chr1_75096893_75098000 501 608 rs11210490 chr1_75096893_75098000:534 G C 108 34 27 True
IISNP112 chr7_130020932_130022055 501 624 rs1126899 chr7_130020932_130022055:557 G C 124 57 43 True
IISNP113 chr15_78632267_78633388 501 622 rs1127472 chr15_78632267_78633388:564 C G 122 64 41 True
IISNP114 chr10_24872787_24873906 501 620 rs1127893 chr10_24872787_24873906:583 C G 120 83 39 False
IISNP115 chr5_176862952_176864062 501 611 rs1130857 chr5_176862952_176864062:568 G C 111 68 30 True
IISNP116 chr4_88415067_88416171 501 605 rs1049544 chr4_88415067_88416171:570 G C 105 70 24 True
IISNP117 chr19_44302506_44303626 501 621 rs11547806 chr19_44302506_44303626:561 C G 121 61 40 True
IISNP118 chr12_121416065_121417194 501 630 rs1169289 chr12_121416065_121417194:558 C G 130 58 49 True
IISNP119 chr9_2717972_2719101 501 630 rs12237048 chr9_2717972_2719101:563 C G 130 63 49 True
IISNP12 chr16_78016473_78017602 501 630 rs430046 chr16_78016473_78017602:579 C T 130 79 49 True
IISNP120 chr4_129042633_129043755 501 623 rs12508837 chr4_129042633_129043755:572 C G 123 72 42 True
IISNP121 chr10_5136059_5137186 501 628 rs12529 chr10_5136059_5137186:593 C G 128 93 47 False
IISNP122 chr6_170861722_170862832 501 611 rs12717 chr6_170861722_170862832:579 G C 111 79 30 True
IISNP123 chr5_161118544_161119671 501 628 rs13184586 chr5_161118544_161119671:582 C G 128 82 47 True
IISNP124 chr9_129455060_129456167 501 608 rs13295990 chr9_129455060_129456167:528 G C 108 28 27 True
IISNP125 chr13_25008849_25009978 501 630 rs13428 chr13_25008849_25009978:593 C G 130 93 49 False
IISNP126 chr19_48620482_48621601 501 620 rs13436 chr19_48620482_48621601:555 C G 120 55 39 True
IISNP127 chr11_57798787_57799916 501 630 rs1374570 chr11_57798787_57799916:585 G C 130 85 49 False
IISNP128 chr3_16305112_16306238 501 627 rs14080 chr3_16305112_16306238:563 C G 127 63 46 True
IISNP129 chr9_125315189_125316306 501 618 rs1411271 chr9_125315189_125316306:590 G C 118 90 37 False
IISNP13 chr19_39559236_39560337 501 602 rs576261 chr19_39559236_39560337:572 A C 102 72 21 True
IISNP130 chr19_618466_619585 501 620 rs14155 chr19_618466_619585:556 G C 120 56 39 True
IISNP131 chr1_247751483_247752601 501 619 rs1151687 chr1_247751483_247752601:537 G C 119 37 38 False
IISNP132 chr12_49255241_49256366 501 626 rs1565933 chr12_49255241_49256366:558 G C 126 58 45 True
IISNP133 chr12_14656198_14657327 501 630 rs1600 chr12_14656198_14657327:571 G C 130 71 49 True
IISNP134 chr6_38781300_38782411 501 612 rs1678690 chr6_38781300_38782411:567 C G 112 67 31 True
IISNP135 chr2_29415814_29416943 501 630 rs1881421 chr2_29415814_29416943:553 G C 130 53 49 True
IISNP136 chr19_44981323_44982437 501 615 rs1897820 chr19_44981323_44982437:561 C G 115 61 34 True
IISNP137 chr15_40655304_40656417 501 614 rs1898882 chr15_40655304_40656417:570 G C 114 70 33 True
IISNP138 chr21_40669882_40670990 501 609 rs2056844 chr21_40669882_40670990:579 G C 109 79 28 True
IISNP139 chr8_23058791_23059898 501 608 rs20575 chr8_23058791_23059898:534 C G 108 34 27 True
IISNP14 chr8_28410486_28411610 501 625 rs10092491 chr8_28410486_28411610:587 T C 125 87 44 False
IISNP140 chr21_47849924_47851051 501 628 rs2070426 chr21_47849924_47851051:561 G C 128 61 47 True
IISNP141 chr6_33272320_33273427 501 608 rs2071888 chr6_33272320_33273427:536 G C 108 36 27 True
IISNP142 chr12_31249317_31250444 501 628 rs2075322 chr12_31249317_31250444:545 C G 128 45 47 False
IISNP143 chr6_52617161_52618275 501 615 rs2180314 chr6_52617161_52618275:571 C G 115 71 34 True
IISNP144 chr6_41773010_41774136 501 627 rs2185798 chr6_41773010_41774136:567 G C 127 67 46 True
IISNP145 chr12_5020815_5021938 501 624 rs2227910 chr12_5020815_5021938:534 G C 124 34 43 False
IISNP146 chr9_137711436_137712561 501 626 rs2228560 chr9_137711436_137712561:562 G C 126 62 45 True
IISNP147 chr2_215644872_215645995 501 624 rs2229571 chr2_215644872_215645995:593 C G 124 93 43 False
IISNP148 chr2_75113219_75114341 501 623 rs2229627 chr2_75113219_75114341:571 C G 123 71 42 True
IISNP149 chr3_129285829_129286957 501 629 rs2245285 chr3_129285829_129286957:585 G C 129 85 48 False
IISNP15 chr16_5868144_5869263 501 620 rs2342747 chr16_5868144_5869263:557 A G 120 57 39 True
IISNP150 chr21_44293171_44294278 501 608 rs2248490 chr21_44293171_44294278:574 C G 108 74 27 True
IISNP151 chr7_150877678_150878790 501 613 rs2253592 chr7_150877678_150878790:583 C G 113 83 32 False
IISNP152 chr1_22216012_22217133 501 622 rs2254357 chr1_22216012_22217133:593 C G 122 93 41 False
IISNP153 chr14_58563143_58564270 501 628 rs2273442 chr14_58563143_58564270:552 G C 128 52 47 True
IISNP154 chr10_99438974_99440086 501 613 rs2275047 chr10_99438974_99440086:568 G C 113 68 32 True
IISNP155 chr12_130940594_130941723 501 630 rs2277361 chr12_130940594_130941723:557 G C 130 57 49 True
IISNP156 chr12_56827164_56828284 501 621 rs2279665 chr12_56827164_56828284:531 C G 121 31 40 False
IISNP157 chr9_8388794_8389902 501 609 rs2279776 chr9_8388794_8389902:571 C G 109 71 28 True
IISNP158 chr22_37963741_37964868 501 628 rs2281098 chr22_37963741_37964868:559 C G 128 59 47 True
IISNP159 chr19_10083723_10084832 501 610 rs2287813 chr19_10083723_10084832:570 C G 110 70 29 True
IISNP16 chr3_32417091_32418199 501 609 rs4364205 chr3_32417091_32418199:554 T G 109 54 28 True
IISNP160 chr17_76448943_76450062 501 620 rs2289751 chr17_76448943_76450062:563 G C 120 63 39 True
IISNP161 chr15_22960301_22961425 501 625 rs2289818 chr15_22960301_22961425:568 G C 125 68 44 True
IISNP162 chr1_87100813_87101939 501 627 rs2292830 chr1_87100813_87101939:563 C G 127 63 46 True
IISNP163 chr8_27667377_27668505 501 629 rs2294092 chr8_27667377_27668505:593 C G 129 93 48 False
IISNP164 chr6_126277677_126278784 501 608 rs2295005 chr6_126277677_126278784:554 G C 108 54 27 True
IISNP165 chr10_90342263_90343376 501 614 rs2296545 chr10_90342263_90343376:575 C G 114 75 33 True
IISNP166 chr7_138739465_138740586 501 622 rs2297236 chr7_138739465_138740586:573 G C 122 73 41 True
IISNP167 chr7_156761669_156762794 501 626 rs2302443 chr7_156761669_156762794:556 G C 126 56 45 True
IISNP168 chr16_88767192_88768321 501 630 rs2306049 chr16_88767192_88768321:578 G C 130 78 49 True
IISNP169 chr22_45821381_45822501 501 621 rs1022478 chr22_45821381_45822501:576 C G 121 76 40 True
IISNP17 chr20_15124404_15125523 501 620 rs445251 chr20_15124404_15125523:530 G C 120 30 39 False
IISNP170 chr17_15216858_15217965 501 608 rs230898 chr17_15216858_15217965:580 C G 108 80 27 True
IISNP171 chr19_36277889_36279010 501 622 rs231235 chr19_36277889_36279010:582 C G 122 82 41 True
IISNP172 chr6_150209159_150210278 501 620 rs2342767 chr6_150209159_150210278:559 C G 120 59 39 True
IISNP173 chr20_5903313_5904421 501 609 rs236152 chr20_5903313_5904421:536 C G 109 36 28 True
IISNP174 chr3_48460757_48461883 501 627 rs2362450 chr3_48460757_48461883:557 C G 127 57 46 True
IISNP175 chr2_27324182_27325292 501 611 rs2384571 chr2_27324182_27325292:543 G C 111 43 30 True
IISNP176 chr5_75932415_75933522 501 608 rs2455230 chr5_75932415_75933522:551 G C 108 51 27 True
IISNP177 chr5_140531170_140532269 501 600 rs246703 chr5_140531170_140532269:577 C G 100 77 19 True
IISNP178 chr10_25700758_25701869 501 612 rs2480345 chr10_25700758_25701869:584 C G 112 84 31 False
IISNP179 chr5_78339702_78340831 501 630 rs248385 chr5_78339702_78340831:556 C G 130 56 49 True
IISNP18 chr9_27985366_27986466 501 601 rs7041158 chr9_27985366_27986466:573 C T 101 73 20 True
IISNP180 chr1_62516111_62517226 501 616 rs2498982 chr1_62516111_62517226:573 G C 116 73 35 True
IISNP181 chr10_38344113_38345242 501 630 rs2505232 chr10_38344113_38345242:588 C G 130 88 49 False
IISNP182 chr11_94230690_94231811 501 622 rs2509943 chr11_94230690_94231811:568 C G 122 68 41 True
IISNP183 chr16_4309882_4311001 501 620 rs251732 chr16_4309882_4311001:587 C G 120 87 39 False
IISNP184 chr9_136536239_136537346 501 608 rs2519123 chr9_136536239_136537346:555 C G 108 55 27 True
IISNP185 chr7_25194102_25195226 501 625 rs2523072 chr7_25194102_25195226:564 G C 125 64 44 True
IISNP186 chr18_44560549_44561667 501 619 rs2571028 chr18_44560549_44561667:552 C G 119 52 38 True
IISNP187 chr11_4566780_4567909 501 630 rs2657167 chr11_4566780_4567909:556 C G 130 56 49 True
IISNP188 chr8_143694218_143695347 501 630 rs28686812 chr8_143694218_143695347:558 G C 130 58 49 True
IISNP189 chr10_126714134_126715248 501 615 rs2946994 chr10_126714134_126715248:581 G C 115 81 34 True
IISNP19 chr1_233447873_233448982 501 610 rs1294331 chr1_233447873_233448982:541 C T 110 41 29 True
IISNP190 chr19_53343564_53344688 501 625 rs10419826 chr19_53343564_53344688:555 C G 125 55 44 True
IISNP191 chr11_125763182_125764289 501 608 rs3088241 chr11_125763182_125764289:565 C G 108 65 27 True
IISNP192 chr17_35901690_35902813 501 624 rs3110623 chr17_35901690_35902813:536 C G 124 36 43 False
IISNP193 chr7_12268849_12269978 501 630 rs3173615 chr7_12268849_12269978:569 C G 130 69 49 True
IISNP194 chr16_11773071_11774198 501 628 rs3190321 chr16_11773071_11774198:592 C G 128 92 47 False
IISNP195 chr22_31490725_31491854 501 630 rs3205187 chr22_31490725_31491854:571 G C 130 71 49 True
IISNP196 chr4_77660183_77661297 501 615 rs344141 chr4_77660183_77661297:549 C G 115 49 34 True
IISNP197 chr4_186379303_186380429 501 627 rs35596415 chr4_186379303_186380429:597 G C 127 97 46 False
IISNP198 chr22_22868645_22869769 501 625 rs362124 chr22_22868645_22869769:565 C G 125 65 44 True
IISNP199 chr19_54663644_54664769 501 626 rs36657 chr19_54663644_54664769:566 G C 126 66 45 True
IISNP2 chr3_113804421_113805528 501 608 rs1872575 chr3_113804421_113805528:559 G A 108 59 27 True
IISNP20 chr5_17374335_17375441 501 607 rs159606 chr5_17374335_17375441:564 A G 107 64 26 True
IISNP200 chr2_219601952_219603075 501 624 rs3731877 chr2_219601952_219603075:548 G C 124 48 43 True
IISNP201 chr2_220378975_220380095 501 621 rs3731909 chr2_220378975_220380095:586 C G 121 86 40 False
IISNP202 chr6_76659989_76661118 501 630 rs3734311 chr6_76659989_76661118:563 G C 130 63 49 True
IISNP203 chr7_20180151_20181280 501 630 rs3735615 chr7_20180151_20181280:567 C G 130 67 49 True
IISNP204 chr10_128018457_128019577 501 621 rs3740199 chr10_128018457_128019577:569 C G 121 69 40 True
IISNP205 chr2_101009515_101010629 501 615 rs3748930 chr2_101009515_101010629:568 G C 115 68 34 True
IISNP206 chr11_8946706_8947820 501 615 rs3751066 chr11_8946706_8947820:578 G C 115 78 34 True
... ... ... ... ... ... ... ... ... ... ... ...
IISNP245 chr11_117163245_117164370 501 626 rs638405 chr11_117163245_117164370:580 C G 126 80 45 True
IISNP246 chr6_56482232_56483352 501 621 rs6459166 chr6_56482232_56483352:570 C G 121 70 40 True
IISNP247 chr6_138412785_138413907 501 623 rs648802 chr6_138412785_138413907:549 G C 123 49 42 True
IISNP248 chr19_57837471_57838600 501 630 rs6510057 chr19_57837471_57838600:548 C G 130 48 49 False
IISNP249 chr3_186917177_186918300 501 624 rs6764714 chr3_186917177_186918300:575 C G 124 75 43 True
IISNP25 chr11_5098168_5099267 501 600 rs10768550 chr11_5098168_5099267:547 C T 100 47 19 True
IISNP250 chr3_14755064_14756187 501 624 rs6790129 chr3_14755064_14756187:554 C G 124 54 43 True
IISNP251 chr3_45052203_45053327 501 625 rs6794 chr3_45052203_45053327:573 G C 125 73 44 True
IISNP252 chr3_183777454_183778574 501 621 rs6807362 chr3_183777454_183778574:557 G C 121 57 40 True
IISNP253 chr4_139139958_139141085 501 628 rs6838248 chr4_139139958_139141085:537 G C 128 37 47 False
IISNP254 chr7_141672808_141673933 501 626 rs713598 chr7_141672808_141673933:538 C G 126 38 45 False
IISNP255 chr14_50798535_50799661 501 627 rs7161563 chr14_50798535_50799661:592 G C 127 92 46 False
IISNP256 chr10_114052989_114054096 501 608 rs726009 chr10_114052989_114054096:558 C G 108 58 27 True
IISNP257 chr1_214836531_214837646 501 616 rs7289 chr1_214836531_214837646:580 C G 116 80 35 True
IISNP258 chr12_14018199_14019328 501 630 rs7301328 chr12_14018199_14019328:579 G C 130 79 49 True
IISNP259 chr13_73348771_73349897 501 627 rs7332388 chr13_73348771_73349897:589 G C 127 89 46 False
IISNP26 chr12_130761129_130762238 501 610 rs10773760 chr12_130761129_130762238:568 A G 110 68 29 True
IISNP260 chr22_51063487_51064595 501 609 rs743616 chr22_51063487_51064595:553 G C 109 53 28 True
IISNP261 chr6_36286765_36287879 501 615 rs743852 chr6_36286765_36287879:548 G C 115 48 34 True
IISNP262 chr17_71232306_71233435 501 630 rs745142 chr17_71232306_71233435:576 G C 130 76 49 True
IISNP263 chr6_46107197_46108304 501 608 rs7451713 chr6_46107197_46108304:556 C G 108 56 27 True
IISNP264 chr1_205553518_205554618 501 601 rs7526132 chr1_205553518_205554618:568 G C 101 68 20 True
IISNP265 chr1_47799106_47800221 501 616 rs7543016 chr1_47799106_47800221:534 G C 116 34 35 False
IISNP266 chr2_28824241_28825363 501 623 rs7601771 chr2_28824241_28825363:553 C G 123 53 42 True
IISNP267 chr7_4026399_4027521 501 623 rs7785899 chr7_4026399_4027521:546 C G 123 46 42 True
IISNP268 chr1_111956532_111957661 501 630 rs7825 chr1_111956532_111957661:566 C G 130 66 49 True
IISNP269 chr14_103439920_103441032 501 613 rs8009219 chr14_103439920_103441032:554 G C 113 54 32 True
IISNP27 chr9_137416746_137417845 501 600 rs10776839 chr9_137416746_137417845:563 G T 100 63 19 True
IISNP270 chr15_94883526_94884639 501 614 rs8025851 chr15_94883526_94884639:583 G C 114 83 33 False
IISNP271 chr16_16278312_16279424 501 613 rs8058696 chr16_16278312_16279424:558 G C 113 58 32 True
IISNP272 chr17_48625341_48626470 501 630 rs8076632 chr17_48625341_48626470:588 C G 130 88 49 False
IISNP273 chr16_8952508_8953628 501 621 rs8097 chr16_8952508_8953628:574 C G 121 74 40 True
IISNP274 chr19_18377056_18378185 501 630 rs8103906 chr19_18377056_18378185:592 G C 130 92 49 False
IISNP275 chr1_17659939_17661046 501 608 rs874881 chr1_17659939_17661046:561 G C 108 61 27 True
IISNP276 chr12_88440104_88441233 501 630 rs9262 chr12_88440104_88441233:573 G C 130 73 49 True
IISNP277 chr3_118866464_118867580 501 617 rs9289122 chr3_118866464_118867580:584 C G 117 84 36 False
IISNP278 chr17_42475406_42476535 501 630 rs936019 chr17_42475406_42476535:578 G C 130 78 49 True
IISNP279 chr6_26508757_26509875 501 619 rs9393728 chr6_26508757_26509875:574 C G 119 74 38 True
IISNP28 chr2_10085153_10086253 501 601 rs1109037 chr2_10085153_10086253:570 G A 101 70 20 True
IISNP280 chr11_60700573_60701681 501 609 rs9513 chr11_60700573_60701681:564 C G 109 64 28 True
IISNP281 chr19_56422500_56423625 501 626 rs977070 chr19_56422500_56423625:575 C G 126 75 45 True
IISNP282 chr3_112642035_112643149 501 615 rs9865242 chr3_112642035_112643149:534 C G 115 34 34 False
IISNP29 chr20_16240863_16241962 501 600 rs12480506 chr20_16240863_16241962:554 A G 100 54 19 True
IISNP3 chr1_160786113_160787219 501 607 rs560681 chr1_160786113_160787219:558 A G 107 58 26 True
IISNP30 chr2_182412681_182413789 501 609 rs12997453 chr2_182412681_182413789:579 A G 109 79 28 True
IISNP31 chr4_76425332_76426441 501 610 rs13134862 chr4_76425332_76426441:565 G A 110 65 29 True
IISNP32 chr6_12059397_12060504 501 608 rs13218440 chr6_12059397_12060504:558 G A 108 58 27 True
IISNP33 chr6_94536699_94537824 501 626 rs1336071 chr6_94536699_94537824:557 T C 126 57 45 True
IISNP34 chr6_123894407_123895512 501 606 rs1358856 chr6_123894407_123895512:572 C A 106 72 25 True
IISNP35 chr10_97172060_97173166 501 607 rs1410059 chr10_97172060_97173166:536 T C 107 36 26 True
IISNP36 chr6_120560128_120561231 501 604 rs1478829 chr6_120560128_120561231:567 T A 104 67 23 True
IISNP37 chr1_4366758_4367875 501 618 rs1490413 chr1_4366758_4367875:566 G A 118 66 37 True
IISNP38 chr11_5708471_5709577 501 607 rs1498553 chr11_5708471_5709577:558 C T 107 58 26 True
IISNP39 chr20_51295583_51296712 501 630 rs1523537 chr20_51295583_51296712:580 T C 130 80 49 True
IISNP4 chr8_144656177_144657285 501 609 rs4606077 chr8_144656177_144657285:578 T C 109 78 28 True
IISNP40 chr4_157489335_157490443 501 609 rs1554472 chr4_157489335_157490443:572 G A 109 72 28 True
IISNP41 chr18_55225209_55226308 501 600 rs1736442 chr18_55225209_55226308:569 T C 100 69 19 True
IISNP42 chr15_39312848_39313954 501 607 rs1821380 chr15_39312848_39313954:555 C G 107 55 26 True
IISNP43 chr4_10968504_10969612 501 609 rs2046361 chr4_10968504_10969612:556 T A 109 56 28 True
IISNP44 chr22_23801605_23802709 501 605 rs2073383 chr22_23801605_23802709:567 T C 105 67 24 True
IISNP45 chr6_152697130_152698240 501 611 rs214955 chr6_152697130_152698240:577 C T 111 77 30 True
IISNP46 chr17_41286243_41287360 501 618 rs2175957 chr17_41286243_41287360:580 T G 118 80 37 True
IISNP47 chr12_6908891_6910000 501 610 rs2255301 chr12_6908891_6910000:552 T C 110 52 29 True
IISNP48 chr12_6945352_6946456 501 605 rs2269355 chr12_6945352_6946456:563 C G 105 63 24 True
IISNP49 chr9_14746585_14747714 501 630 rs2270529 chr9_14746585_14747714:549 T C 130 49 49 False
IISNP5 chr12_40862467_40863585 501 619 rs2920816 chr12_40862467_40863585:586 A G 119 86 38 False
IISNP50 chr6_148760890_148761999 501 610 rs2272998 chr6_148760890_148761999:567 G C 110 67 29 True
IISNP51 chr17_80525564_80526669 501 606 rs2291395 chr17_80525564_80526669:576 A G 106 76 25 True
IISNP52 chr17_80765219_80766321 501 603 rs2292972 chr17_80765219_80766321:570 T C 103 70 22 True
IISNP53 chr3_110300565_110301664 501 600 rs2399332 chr3_110300565_110301664:562 T G 100 62 19 True
IISNP54 chr6_127462805_127463913 501 609 rs2503107 chr6_127462805_127463913:572 C A 109 72 28 True
IISNP55 chr20_23016527_23017635 501 609 rs2567608 chr20_23016527_23017635:556 T C 109 56 28 True
IISNP56 chr6_55155134_55156239 501 606 rs2811231 chr6_55155134_55156239:571 C A 106 71 25 True
IISNP57 chr21_33582165_33583274 501 610 rs2833736 chr21_33582165_33583274:558 G A 110 58 29 True
IISNP58 chr5_169735367_169736476 501 610 rs315791 chr5_169735367_169736476:554 A C 110 54 29 True
IISNP59 chr7_137029274_137030380 501 607 rs321198 chr7_137029274_137030380:565 T C 107 65 26 True
IISNP6 chr7_4309792_4310920 501 629 rs6955448 chr7_4309792_4310920:574 C T 129 74 48 True
IISNP60 chr5_178690152_178691259 501 608 rs338882 chr5_178690152_178691259:574 G A 108 74 27 True
IISNP61 chr17_80739299_80740406 501 608 rs3744163 chr17_80739299_80740406:561 G C 108 61 27 True
IISNP62 chr10_17192789_17193898 501 610 rs3780962 chr10_17192789_17193898:558 A G 110 58 29 True
IISNP63 chr8_136838646_136839775 501 630 rs4288409 chr8_136838646_136839775:584 A C 130 84 49 False
IISNP64 chr14_104768569_104769678 501 610 rs4530059 chr14_104768569_104769678:581 G A 110 81 29 True
IISNP65 chr21_28022802_28023902 501 601 rs464663 chr21_28022802_28023902:569 T C 101 69 20 True
IISNP66 chr17_80531082_80532207 501 626 rs4789798 chr17_80531082_80532207:562 C G 126 62 45 True
IISNP67 chr17_6810940_6812066 501 627 rs4796362 chr17_6810940_6812066:590 G A 127 90 46 False
IISNP68 chr1_105717077_105718184 501 608 rs4847034 chr1_105717077_105718184:555 A G 108 55 27 True
IISNP69 chr18_47370442_47371541 501 600 rs521861 chr18_47370442_47371541:573 C G 100 73 19 True
IISNP7 chr13_100037637_100038761 501 625 rs1058083 chr13_100037637_100038761:597 A G 125 97 44 False
IISNP70 chr22_19920061_19921192 501 632 rs5746846 chr22_19920061_19921192:586 C G 132 86 51 False
IISNP71 chr11_122195414_122196543 501 630 rs590162 chr11_122195414_122196543:576 C T 130 76 49 True
IISNP72 chr3_193206814_193207921 501 608 rs6444724 chr3_193206814_193207921:567 T C 108 67 27 True
IISNP73 chr11_105912429_105913529 501 601 rs6591147 chr11_105912429_105913529:556 T C 101 56 20 True
IISNP74 chr17_80715140_80716246 501 607 rs689512 chr17_80715140_80716246:563 G C 107 63 26 True
IISNP75 chr16_7519685_7520809 501 625 rs7205345 chr16_7519685_7520809:570 C G 125 70 44 True
IISNP76 chr14_53216148_53217276 501 629 rs722290 chr14_53216148_53217276:576 G C 129 76 48 True
IISNP77 chr18_22738427_22739556 501 630 rs7229946 chr18_22738427_22739556:575 G A 130 75 49 True
IISNP78 chr10_118506324_118507433 501 610 rs740598 chr10_118506324_118507433:576 G A 110 76 29 True
IISNP79 chr1_14154833_14155962 501 630 rs7520386 chr1_14154833_14155962:570 G A 130 70 49 True
IISNP8 chr21_43606463_43607573 501 611 rs221956 chr21_43606463_43607573:535 T C 111 35 30 True
IISNP80 chr5_159487382_159488507 501 626 rs7704770 chr5_159487382_159488507:572 G A 126 72 45 True
IISNP81 chr17_41341424_41342523 501 600 rs8070085 chr17_41341424_41342523:561 A G 100 61 19 True
IISNP82 chr17_80461344_80462465 501 622 rs8078417 chr17_80461344_80462465:592 C T 122 92 41 False
IISNP83 chr1_239881353_239882471 501 619 rs891700 chr1_239881353_239882471:574 A G 119 74 38 True
IISNP84 chr11_11095660_11096769 501 610 rs901398 chr11_11095660_11096769:562 C T 110 62 29 True
IISNP85 chr13_84456181_84457286 501 606 rs9546538 chr13_84456181_84457286:555 T C 106 55 25 True
IISNP86 chr22_19919790_19920889 501 600 rs9606186 chr22_19919790_19920889:570 C G 100 70 19 True
IISNP87 chr18_29310484_29311587 501 604 rs985492 chr18_29310484_29311587:551 G A 104 51 23 True
IISNP88 chr3_59487752_59488863 501 612 rs9866013 chr3_59487752_59488863:589 T C 112 89 31 False
IISNP89 chr22_33558944_33560052 501 609 rs987640 chr22_33558944_33560052:565 T A 109 65 28 True
IISNP9 chr5_136632784_136633892 501 609 rs13182883 chr5_136632784_136633892:555 G A 109 55 28 True
IISNP90 chr17_2918812_2919921 501 610 rs9905977 chr17_2918812_2919921:582 A G 110 82 29 True
IISNP91 chr2_124108634_124109748 501 615 rs993934 chr2_124108634_124109748:580 A G 115 80 34 True
IISNP92 chr18_9749309_9750416 501 608 rs9951171 chr18_9749309_9750416:571 G A 108 71 27 True
IISNP93 chr7_47924777_47925902 501 626 rs10274334 chr7_47924777_47925902:555 C G 126 55 45 True
IISNP94 chr19_57085220_57086327 501 608 rs10421285 chr19_57085220_57086327:550 G C 108 50 27 True
IISNP95 chr19_41938759_41939869 501 611 rs1043413 chr19_41938759_41939869:539 C G 111 39 30 True
IISNP96 chr1_19447280_19448406 501 627 rs1044010 chr1_19447280_19448406:564 C G 127 64 46 True
IISNP97 chr8_142203762_142204884 501 623 rs1045248 chr8_142203762_142204884:565 C G 123 65 42 True
IISNP98 chr14_31354504_31355624 501 621 rs1045644 chr14_31354504_31355624:593 C G 121 93 40 False
IISNP99 chr11_58318053_58319181 501 629 rs1047979 chr11_58318053_58319181:567 C G 129 67 48 True

282 rows × 11 columns

In [61]:
namedtuple()
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-61-726b1c1dd7f6> in <module>()
----> 1 namedtuple()

NameError: name 'namedtuple' is not defined
In [ ]:
snp_annots = defaultdict(namedtuple)
In [131]:
df_bySNP.groupby('SNP_NAME').ALL_READS.mean().sort_values()[:20].iplot(kind='barh',)# annotations=snp_annots)#, figsize=(10,16))#, rot=30)
In [78]:
df_all_AV_blanks.PCT_DD_CFDNA.plot(kind='hist', ec='k', lw=1.5, fc='w', bins=20, label=str(df_all_AV_blanks.PCT_DD_CFDNA.describe()), legend='right')
plt.gca().legend(loc='best',
               bbox_to_anchor=(1, 1))
sns.despine(offset=10, trim=True)
sns.set_style('ticks')
In [17]:
df_all_AV_blanks.QC_RESULT.describe()

# .PCT_DD_CFDNA.plot(kind='hist', ec='k', lw=1.5, fc='w', bins=20, label=str(df_all_AV_blanks.PCT_DD_CFDNA.describe()), legend='right')
# plt.gca().legend(loc='best',
#                bbox_to_anchor=(1, 1))
# sns.despine(offset=10, trim=True)
# sns.set_style('ticks')
Out[17]:
count      180
unique       1
top       PASS
freq       180
Name: QC_RESULT, dtype: object
In [121]:
return_numeric(df_all).hist(fc='k', ec='r', lw=1.0, bins=30, alpha=0.5, figsize=(24,8), layout=(2,5), xrot=30)# sharey=True, )
sns.despine(offset=10)
sns.set_style('ticks')
In [116]:
return_numeric(df_all).corr()
Out[116]:
CLUSTER_DENSITY ID PCT_DD_CFDNA READS_PASS_QC SNPS_PASS_QC TOTAL_READS
CLUSTER_DENSITY 1.000000 -0.438208 0.035895 0.111602 -0.018882 0.112193
ID -0.438208 1.000000 -0.169445 -0.052886 0.023769 -0.053741
PCT_DD_CFDNA 0.035895 -0.169445 1.000000 -0.059137 -0.448501 -0.058069
READS_PASS_QC 0.111602 -0.052886 -0.059137 1.000000 0.618406 0.999925
SNPS_PASS_QC -0.018882 0.023769 -0.448501 0.618406 1.000000 0.614255
TOTAL_READS 0.112193 -0.053741 -0.058069 0.999925 0.614255 1.000000
In [121]:
df_all.PCT_DD_CFDNA.clip_upper(0.01).mean()
Out[121]:
0.00020777777777777792
In [123]:
# Gather via input list DART_patient_IDs linked by unique Sample_Name 
# --> insert into existing df_all_DART to replace nan's in current PATIENT_ID col
# df_DART_PIDs = pd.read_csv(DART_lock2_PIDs)
# df_DART_PIDs

# ## DART STUDY
# DART_PIDs = {}
# DART_PID_to_EID = defaultdict(list)
# # for i,(eid,pid) in enumerate(zip(df_all_DART.index, df_all_DART.PATIENT_STUDY_ID)):
# for pid,eid in zip(df_DART_PIDs.SITE_SUBJECT_ID, df_DART_PIDs.SAMPLE_NAME):
#     DART_PIDs[eid] = pid
#     DART_PID_to_EID[pid].append(eid)
# # DART_PIDs.items()

# df_DART_bySNP.describe(include='all')
# df_QC_Eval_bySNP.describe(include='all')
# print(sorted(df_DART_bySNP.SNP_NAME.unique()))
# len(sorted(df_DART_bySNP.SNP_NAME.unique()))
In [65]:
# help(pd.DataFrame.set_index)
In [66]:
# help(pd.DataFrame.plot)
In [42]:
df_bySNP.loc[df_bySNP.SNP_NAME=='IISNP145',:]
Out[42]:
ID RUN_ID EXPERIMENT_NAME AMPLICON_NAME SNP_NAME CHROMOSOME POSITION REF ALT REF_COUNT ALT_COUNT REF_FREQ ALT_FREQ REF_ALT_READS ALL_READS ERR_COUNT ERR_FREQ_TOTAL CHROMOSOME_MOCK POSITION_MOCK DONORFREQUENCY ALT_FREQ_TOTAL REF_FREQ_TOTAL DONORFREQUENCYTOTAL RECIPIENTALLELE DONORALLELE SUBSTITUTION SNPDIRECTION SAMPLE_PROJECT UNIQUEID RELATIVE_COVERAGE REFALTFRACTION SNPPASSQC BACKGROUND ADJUSTEDFREQUENCY RECIPIENTGENOCALL ERR_FREQ_FIXED
SAMPLE_NAME
Streck0008-Oct-22-15 2141.0 248.0 PS20151022P1 aIISNP145 IISNP145 chr12 5021348.0 G C 3900.0 3833.0 0.504332 0.495668 7733.0 8128.0 395.0 0.048597 chr12_5020815_5021938 534.0 0.495668 0.47158 0.479823 0.47158 G C GC IISNP145 GC NaN Streck0008-Oct-22-15 1.550679 0.951403 True 0.000174 0.495494 Recipient Hetero 0.544091
In [20]:
# !pip install cufflinks
In [111]:
df_bySNP.UNIQUEID.describe()
Out[111]:
count                    46847
unique                     180
top       HRZ-6-9-60-Oct-7-15 
freq                       262
Name: UNIQUEID, dtype: object

SNP error & background stats

In [122]:
# ax = df_bySNP.ERR_FREQ_TOTAL.groupby(df_bySNP.SNP_NAME).mean().nlargest(20)#.plot('barh', figsize=(10,25), )#, grid=True, fc='w', alpha=0.75, ec='b', lw=5)
sns.set_style('ticks')
df_bySNP['ERR_FREQ_FIXED'] = df_bySNP['ERR_FREQ_TOTAL'] + df_bySNP['DONORFREQUENCY']
df_bySNP.ERR_FREQ_FIXED.describe()
/Users/jcollins-macbook/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:3: SettingWithCopyWarning:


A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy

Out[122]:
count    493905.000000
mean          0.211878
std           0.223675
min           0.000000
25%           0.001368
50%           0.048187
75%           0.465293
max           1.493711
Name: ERR_FREQ_FIXED, dtype: float64
In [107]:
SNP_cov['SNP_NAME'] = SNP_cov.index
In [125]:
# df_bySNP_numeric.sort_index(inplace=True, axis=1)
AV_SNP_stats = df_bySNP.groupby(df_bySNP['SNP_NAME']).describe().unstack()
In [126]:
missing_snps = SNP_cov[~SNP_cov.index.isin(AV_SNP_stats.index)]
In [128]:
for ghost_snp in missing_snps.index:
    AV_SNP_stats.loc[ghost_snp,:] = np.nan
In [129]:
AV_SNP_stats.index
Out[129]:
Index(['IISNP1', 'IISNP10', 'IISNP100', 'IISNP101', 'IISNP102', 'IISNP103', 'IISNP104', 'IISNP105',
       'IISNP106', 'IISNP107',
       ...
       'IISNP220', 'IISNP223', 'IISNP240', 'IISNP280', 'IISNP33', 'IISNP37', 'IISNP44', 'IISNP5',
       'IISNP61', 'IISNP77'],
      dtype='object', name='SNP_NAME', length=282)
In [130]:
AV_SNP_stats.to_csv('AV_N=1927_stats_170412.csv')
In [127]:
missing_snps
Out[127]:
Genome_location Ref_start_pos Ref_end_pos rsID SNP_pos_in_ref Ref Alt amp_length SNP_pos SNP_cov_end_bound SNP_cov_type SNP_NAME
SNP_ID
IISNP118 chr12_121416065_121417194 501 630 rs1169289 chr12_121416065_121417194:558 C G 130 58 49 True IISNP118
IISNP141 chr6_33272320_33273427 501 608 rs2071888 chr6_33272320_33273427:536 G C 108 36 27 True IISNP141
IISNP153 chr14_58563143_58564270 501 628 rs2273442 chr14_58563143_58564270:552 G C 128 52 47 True IISNP153
IISNP155 chr12_130940594_130941723 501 630 rs2277361 chr12_130940594_130941723:557 G C 130 57 49 True IISNP155
IISNP18 chr9_27985366_27986466 501 601 rs7041158 chr9_27985366_27986466:573 C T 101 73 20 True IISNP18
IISNP183 chr16_4309882_4311001 501 620 rs251732 chr16_4309882_4311001:587 C G 120 87 39 False IISNP183
IISNP201 chr2_220378975_220380095 501 621 rs3731909 chr2_220378975_220380095:586 C G 121 86 40 False IISNP201
IISNP220 chr5_113697957_113699073 501 617 rs40179 chr5_113697957_113699073:588 G C 117 88 36 False IISNP220
IISNP223 chr2_26698552_26699653 501 602 rs4335905 chr2_26698552_26699653:575 C G 102 75 21 True IISNP223
IISNP240 chr11_85436305_85437424 501 620 rs597480 chr11_85436305_85437424:564 G C 120 64 39 True IISNP240
IISNP280 chr11_60700573_60701681 501 609 rs9513 chr11_60700573_60701681:564 C G 109 64 28 True IISNP280
IISNP33 chr6_94536699_94537824 501 626 rs1336071 chr6_94536699_94537824:557 T C 126 57 45 True IISNP33
IISNP37 chr1_4366758_4367875 501 618 rs1490413 chr1_4366758_4367875:566 G A 118 66 37 True IISNP37
IISNP44 chr22_23801605_23802709 501 605 rs2073383 chr22_23801605_23802709:567 T C 105 67 24 True IISNP44
IISNP5 chr12_40862467_40863585 501 619 rs2920816 chr12_40862467_40863585:586 A G 119 86 38 False IISNP5
IISNP61 chr17_80739299_80740406 501 608 rs3744163 chr17_80739299_80740406:561 G C 108 61 27 True IISNP61
IISNP77 chr18_22738427_22739556 501 630 rs7229946 chr18_22738427_22739556:575 G A 130 75 49 True IISNP77
In [ ]:
 
In [44]:
high = df_bySNP.ERR_FREQ_FIXED.groupby(df_bySNP.SNP_NAME).mean().nlargest(50)#.plot('barh', figsize=(10,25), )
high_snps = df_bySNP[df_bySNP.SNP_NAME.isin(high.index)]
In [40]:
high_snps_stats = high_snps.ERR_FREQ_FIXED.groupby(high_snps.SNP_NAME).describe().unstack()#.plot('barh', figsize=(8,30))
# high_snps_stats.drop('count', axis=1).sort_values(by='mean').iplot(by='index', kind='bar', figsize=(25,10), grid=True, logy=True,)
high_snps_stats.loc[:,['max', 'min', 'mean', '25%', '50%', '75%', 'std']].sort_values(by='50%').iplot(
    kind='bar', title="AV Blanks - Error frequency stats", theme='ggplot', logy=False, orientation='horizontal', sortbars=True,
    )#, figsize=(25,10), grid=True, logy=True,)
/Users/jcollins-macbook/anaconda3/lib/python3.6/site-packages/cufflinks/plotlytools.py:123: FutureWarning:

sort is deprecated, use sort_values(inplace=True) for INPLACE sorting

In [118]:
df_snp_stats = df_bySNP.groupby('SNP_NAME').describe().unstack()
In [71]:
# df_all.sort_values(by='RUN_DATE',inplace=True)
# df_all.reset_index(inplace=True)
# df_all.loc[:,['RUN_DATE','RUN_NAME','SAMPLENAME']]
In [99]:
# df_bySNP_numeric = df_bySNP.select_dtypes(['float64'])#.columns
# df_bySNP_numeric = df_bySNP_numeric.loc[:,['REF_COUNT', 'ALT_COUNT', 'REF_FREQ', 'ALT_FREQ', 'REF_ALT_READS', 'ALL_READS', 'ERR_COUNT', 'ERR_FREQ_TOTAL', 'DONORFREQUENCY', 'ALT_FREQ_TOTAL', 'REF_FREQ_TOTAL', 'DONORFREQUENCYTOTAL', 'RELATIVE_COVERAGE', 'REFALTFRACTION', 'BACKGROUND', 'ADJUSTEDFREQUENCY', 'ERR_FREQ_FIXED']]                                  
# # df_bySNP_numeric
In [97]:
# AV_SNP_stats.to_csv('AV_SNP_error_background(+more)_general_stats.csv')
In [101]:
AV_SNP_stats.to_csv('AV_SNP_error_background(+more)_general_stats.csv')
In [25]:
AV_SNP_stats.columns
Out[25]:
MultiIndex(levels=[['ADJUSTEDFREQUENCY', 'ALL_READS', 'ALT_COUNT', 'ALT_FREQ', 'ALT_FREQ_TOTAL', 'BACKGROUND', 'DONORFREQUENCY', 'DONORFREQUENCYTOTAL', 'ERR_COUNT', 'ERR_FREQ_FIXED', 'ERR_FREQ_TOTAL', 'REFALTFRACTION', 'REF_ALT_READS', 'REF_COUNT', 'REF_FREQ', 'REF_FREQ_TOTAL', 'RELATIVE_COVERAGE'], ['count', 'mean', 'std', 'min', '25%', '50%', '75%', 'max']],
           labels=[[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16], [0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4, 5, 6, 7]])
In [40]:
help(pd.DataFrame.nlargest)
Help on function nlargest in module pandas.core.frame:

nlargest(self, n, columns, keep='first')
    Get the rows of a DataFrame sorted by the `n` largest
    values of `columns`.
    
    .. versionadded:: 0.17.0
    
    Parameters
    ----------
    n : int
        Number of items to retrieve
    columns : list or str
        Column name or names to order by
    keep : {'first', 'last', False}, default 'first'
        Where there are duplicate values:
        - ``first`` : take the first occurrence.
        - ``last`` : take the last occurrence.
    
    Returns
    -------
    DataFrame
    
    Examples
    --------
    >>> df = DataFrame({'a': [1, 10, 8, 11, -1],
    ...                 'b': list('abdce'),
    ...                 'c': [1.0, 2.0, np.nan, 3.0, 4.0]})
    >>> df.nlargest(3, 'a')
        a  b   c
    3  11  c   3
    1  10  b   2
    2   8  d NaN

In [132]:
AV_SNP_stats.BACKGROUND.nlargest(20, columns=['mean']).drop(['count'],axis=1).iplot(kind='bar', title="AV Blanks - Background stats", 
                                        theme='ggplot', logy=False, orientation='horizontal', sortbars=True,)
/Users/jcollins-macbook/anaconda3/lib/python3.6/site-packages/cufflinks/plotlytools.py:123: FutureWarning:

sort is deprecated, use sort_values(inplace=True) for INPLACE sorting

In [45]:
AV_SNP_stats.BACKGROUND.describe()
Out[45]:
count mean std min 25% 50% 75% max
count 265.000000 258.000000 256.000000 258.000000 258.000000 258.000000 258.000000 258.000000
mean 143.649057 0.000421 0.000075 0.000294 0.000362 0.000412 0.000473 0.000606
std 41.298725 0.000464 0.000105 0.000296 0.000385 0.000454 0.000540 0.000715
min 0.000000 0.000167 0.000016 0.000121 0.000153 0.000162 0.000167 0.000167
25% 157.000000 0.000179 0.000018 0.000143 0.000165 0.000179 0.000191 0.000220
50% 160.000000 0.000180 0.000019 0.000144 0.000166 0.000180 0.000193 0.000235
75% 160.000000 0.000271 0.000036 0.000148 0.000174 0.000202 0.000330 0.000435
max 160.000000 0.001575 0.000337 0.001055 0.001496 0.001606 0.001750 0.002116
In [47]:
AV_SNP_stats.ADJUSTEDFREQUENCY.nlargest(20, columns=['mean']).drop(['count'],axis=1).iplot(kind='bar', title="AV Blanks - AdjFreq stats", 
                                        theme='ggplot', logy=False, orientation='horizontal', sortbars=True,)
/Users/jcollins-macbook/anaconda3/lib/python3.6/site-packages/cufflinks/plotlytools.py:123: FutureWarning:

sort is deprecated, use sort_values(inplace=True) for INPLACE sorting

In [48]:
AV_SNP_stats.ADJUSTEDFREQUENCY.nsmallest(20, columns=['mean']).drop(['count'],axis=1).iplot(kind='bar', title="AV Blanks - AdjFreq stats", 
                                        theme='ggplot', logy=False, orientation='horizontal', sortbars=True,)
/Users/jcollins-macbook/anaconda3/lib/python3.6/site-packages/cufflinks/plotlytools.py:123: FutureWarning:

sort is deprecated, use sort_values(inplace=True) for INPLACE sorting

In [49]:
AV_SNP_stats.ADJUSTEDFREQUENCY.describe()
Out[49]:
count mean std min 25% 50% 75% max
count 265.000000 258.000000 256.000000 258.000000 258.000000 258.000000 258.000000 258.000000
mean 143.649057 0.205619 0.209457 0.001465 0.020342 0.159086 0.408443 0.480898
std 41.298725 0.079875 0.039569 0.030894 0.081386 0.201397 0.136541 0.077068
min 0.000000 -0.000167 0.000301 -0.002116 -0.001414 -0.001006 -0.000167 -0.000167
25% 157.000000 0.151772 0.202986 -0.000349 -0.000167 0.000317 0.426659 0.497523
50% 160.000000 0.206468 0.220219 -0.000219 0.000023 0.001235 0.464285 0.498968
75% 160.000000 0.251562 0.231617 -0.000210 0.000325 0.409708 0.480335 0.499542
max 160.000000 0.495494 0.242007 0.495494 0.495494 0.495494 0.495494 0.499840
In [ ]:
!jupyter nbconvert --to slides AlloSure_SNP_error_analysis_160412.ipynb